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 pdb1cs0.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 : 0.294
CA-only RMS fit for the two chains : 0.167

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 : 0.362
CA-only RMS fit for the two chains : 0.247

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 : 0.360
CA-only RMS fit for the two chains : 0.252

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 : 0.280
CA-only RMS fit for the two chains : 0.157

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 : 0.319
CA-only RMS fit for the two chains : 0.169

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: 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.

5769 ADP   (5000-)  A  -
5770 ADP   (5006-)  A  -
5771 ORN   (5010-)  A  -
5772 NET   (5094-)  A  -
5792 ADP   (5023-)  C  -
5793 ADP   (5029-)  C  -
5794 ORN   (5033-)  C  -
5795 NET   (5034-)  C  -
5817 ADP   (5046-)  E  -
5818 ADP   (5052-)  E  -
5819 ORN   (5056-)  E  -
5820 NET   (5057-)  E  -
5840 ADP   (5071-)  G  -
5845 NET   (5082-)  G  -
5846 ORN   (5081-)  G  -
5847 ADP   (5077-)  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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

1326 CYG   ( 269-)  B
2763 CYG   ( 269-)  D
4200 CYG   ( 269-)  F
5637 CYG   ( 269-)  H

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 : 3.893 over 35583 bonds
Average difference in B over a bond : 9.82
RMS difference in B over a bond : 14.03

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

  42 TYR   (  42-)  A
  65 TYR   (  65-)  A
 216 TYR   ( 216-)  A
 261 TYR   ( 261-)  A
 330 TYR   ( 330-)  A
 354 TYR   ( 354-)  A
 438 TYR   ( 438-)  A
 526 TYR   ( 526-)  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
1981 TYR   ( 544-)  C
1984 TYR   ( 547-)  C
2054 TYR   ( 617-)  C
And so on for a total of 62 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
1072 PHE   (  15-)  B
1149 PHE   (  92-)  B
1207 PHE   ( 150-)  B
1249 PHE   ( 192-)  B
1405 PHE   ( 348-)  B
1601 PHE   ( 164-)  C
1625 PHE   ( 188-)  C
1674 PHE   ( 237-)  C
1723 PHE   ( 286-)  C
1785 PHE   ( 348-)  C
1846 PHE   ( 409-)  C
1890 PHE   ( 453-)  C
1973 PHE   ( 536-)  C
2274 PHE   ( 852-)  C
2346 PHE   ( 924-)  C
And so on for a total of 67 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
 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
 592 ASP   ( 592-)  A
And so on for a total of 253 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
  81 GLU   (  81-)  A
 101 GLU   ( 101-)  A
 103 GLU   ( 103-)  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
 473 GLU   ( 473-)  A
 474 GLU   ( 474-)  A
And so on for a total of 274 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.

 186 GLU   ( 186-)  A      CD   OE2   1.33    4.0
 217 GLU   ( 217-)  A      CD   OE2   1.33    4.2
 353 ASP   ( 353-)  A      CG   OD1   1.33    4.2
 441 ASP   ( 441-)  A      CG   OD1   1.33    4.0
 624 GLU   ( 624-)  A      CD   OE1   1.33    4.4
 633 GLU   ( 633-)  A      CD   OE1   1.33    4.3
 655 GLU   ( 655-)  A      CD   OE1   1.34    4.5
 743 ASP   ( 758-)  A      CG   OD1   1.33    4.2
 750 ASP   ( 765-)  A      CG   OD1   1.33    4.2
 792 ASP   ( 807-)  A      CG   OD1   1.33    4.3
 994 GLU   (1009-)  A      CD   OE1   1.33    4.1
1052 GLU   (1067-)  A      CD   OE1   1.33    4.0
1124 ASP   (  67-)  B      CG   OD1   1.33    4.5
1291 ASP   ( 234-)  B      CG   OD2   1.33    4.2
1419 ASP   ( 362-)  B      CG   OD1   1.33    4.3
1499 ASP   (  62-)  C      CG   OD2   1.34    4.6
1546 GLU   ( 109-)  C      CD   OE1   1.33    4.2
1624 GLU   ( 187-)  C      CD   OE2   1.33    4.2
1644 ASP   ( 207-)  C      CG   OD1   1.33    4.1
1683 ASP   ( 246-)  C      CG   OD1   1.33    4.3
2029 ASP   ( 592-)  C      CG   OD1   1.33    4.0
2092 GLU   ( 655-)  C      CD   OE1   1.33    4.1
2111 ASP   ( 674-)  C      CG   OD2   1.33    4.3
2113 GLU   ( 676-)  C      CD   OE2   1.33    4.1
2180 ASP   ( 758-)  C      CG   OD1   1.33    4.2
And so on for a total of 92 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

 |  1.001603  0.000188  0.000135|
 |  0.000188  1.000905 -0.000198|
 |  0.000135 -0.000198  1.001191|
Proposed new scale matrix

 |  0.006581 -0.000001  0.000000|
 | -0.000001  0.006099  0.000001|
 |  0.000000  0.000000  0.003003|
With corresponding cell

    A    = 151.942  B   = 163.948  C    = 332.953
    Alpha=  90.013  Beta=  90.003  Gamma=  89.978

The CRYST1 cell dimensions

    A    = 151.700  B   = 163.800  C    = 332.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 287.538
(Under-)estimated Z-score: 12.497

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.

  26 PHE   (  26-)  A      CA   CB   CG  107.37   -6.4
  38 ARG   (  38-)  A      CD   NE   CZ  131.20    5.3
  39 GLU   (  39-)  A      N    CA   CB  117.38    4.0
  39 GLU   (  39-)  A      C    CA   CB   98.25   -6.2
  95 ALA   (  95-)  A      N    CA   CB  117.05    4.4
 149 ALA   ( 149-)  A      N    CA   CB  118.40    5.3
 160 ALA   ( 160-)  A      C    CA   CB  116.76    4.2
 164 PHE   ( 164-)  A      CA   CB   CG  109.35   -4.5
 172 PHE   ( 172-)  A      CA   CB   CG  106.80   -7.0
 173 THR   ( 173-)  A      N    CA   CB  118.55    4.7
 210 LEU   ( 210-)  A      N    CA   CB  117.86    4.3
 266 ASN   ( 266-)  A      CA   CB   CG  118.77    6.2
 286 PHE   ( 286-)  A      C    CA   CB  100.82   -4.9
 289 ASN   ( 289-)  A      CA   CB   CG  108.10   -4.5
 339 ILE   ( 339-)  A      N    CA   CB  118.67    4.8
 364 PHE   ( 364-)  A      CA   CB   CG  107.81   -6.0
 367 PHE   ( 367-)  A      CA   CB   CG  105.72   -8.1
 410 ASP   ( 410-)  A      CA   CB   CG  108.16   -4.4
 417 ASP   ( 417-)  A      CA   CB   CG  119.44    6.8
 450 ASP   ( 450-)  A      CA   CB   CG  117.93    5.3
 453 PHE   ( 453-)  A      CA   CB   CG  109.00   -4.8
 468 GLU   ( 468-)  A      CB   CG   CD  121.40    5.2
 468 GLU   ( 468-)  A      CG   CD   OE2  99.93   -8.0
 468 GLU   ( 468-)  A      CG   CD   OE1 133.65    6.6
 497 PHE   ( 497-)  A      CA   CB   CG  109.78   -4.0
And so on for a total of 344 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
  81 GLU   (  81-)  A
  84 ASP   (  84-)  A
 101 GLU   ( 101-)  A
 103 GLU   ( 103-)  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.

  46 LEU   (  46-)  A      CA    -6.6    24.12    34.19
 149 ALA   ( 149-)  A      CA    -7.0    25.23    34.09
 339 ILE   ( 339-)  A      CA    -7.3    22.16    33.24
 420 ALA   ( 420-)  A      CA    -6.7    25.53    34.09
 435 ARG   ( 435-)  A      CA    -6.8    22.79    33.91
 548 GLU   ( 548-)  A      CA    -7.7    21.28    33.96
 719 GLU   ( 726-)  A      CA    -7.5    21.70    33.96
 984 PRO   ( 999-)  A      N     -9.6   -33.90    -2.48
1195 PRO   ( 138-)  B      N     -6.8   -24.92    -2.48
1421 ALA   ( 364-)  B      CA    -6.8    25.43    34.09
1776 ILE   ( 339-)  C      CA   -16.2     8.75    33.24
1872 ARG   ( 435-)  C      CA    -8.4    20.15    33.91
1995 ASP   ( 558-)  C      CA     6.3    46.25    33.73
2103 PRO   ( 666-)  C      N     -6.7   -24.58    -2.48
2328 LEU   ( 906-)  C      CA    -9.0    20.44    34.19
2413 VAL   ( 991-)  C      CA   -14.9    11.58    33.23
2423 ILE   (1001-)  C      CB     6.8    41.18    32.31
3213 ILE   ( 339-)  E      CA    -8.3    20.71    33.24
3422 GLU   ( 548-)  E      CA    -6.3    23.65    33.96
3936 ALA   (   5-)  F      CA    -6.2    26.21    34.09
4151 PRO   ( 220-)  F      N     -7.0   -25.42    -2.48
4357 LEU   (  46-)  G      CA    -8.1    21.75    34.19
4650 ILE   ( 339-)  G      CA    -9.6    18.73    33.24
5290 VAL   ( 994-)  G      CA    -6.5    23.77    33.23
5297 ILE   (1001-)  G      CB     6.3    40.50    32.31
5550 PRO   ( 182-)  H      N      6.9    20.02    -2.48
The average deviation= 1.533

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.

3213 ILE   ( 339-)  E    6.91
1776 ILE   ( 339-)  C    6.43
4650 ILE   ( 339-)  G    6.40
5297 ILE   (1001-)  G    5.68
4338 ASP   (  27-)  G    5.55
 339 ILE   ( 339-)  A    5.40
4392 GLU   (  81-)  G    5.33
4630 ILE   ( 319-)  G    4.94
5146 VAL   ( 850-)  G    4.77
5667 ASP   ( 299-)  H    4.68
1146 ALA   (  89-)  B    4.67
3652 ALA   ( 793-)  E    4.62
4123 PHE   ( 192-)  F    4.62
1591 GLU   ( 154-)  C    4.56
3486 THR   ( 612-)  E    4.52
 435 ARG   ( 435-)  A    4.49
3830 LEU   ( 971-)  E    4.39
4923 THR   ( 612-)  G    4.34
2088 ALA   ( 651-)  C    4.32
 159 ALA   ( 159-)  A    4.31
1980 MET   ( 543-)  C    4.29
 456 THR   ( 456-)  A    4.27
2856 ASP   ( 362-)  D    4.26
4746 ARG   ( 435-)  G    4.24
 432 GLY   ( 432-)  A    4.19
5687 ALA   ( 319-)  H    4.18
2583 ALA   (  89-)  D    4.16
 986 ILE   (1001-)  A    4.12
1481 VAL   (  44-)  C    4.11
3294 ALA   ( 420-)  E    4.11
5089 ALA   ( 793-)  G    4.10
4230 ASP   ( 299-)  F    4.09
 810 LEU   ( 825-)  A    4.09
1872 ARG   ( 435-)  C    4.08
4355 VAL   (  44-)  G    4.05
3330 THR   ( 456-)  E    4.05
4675 PHE   ( 364-)  G    4.04
3520 THR   ( 646-)  E    4.02
1857 ALA   ( 420-)  C    4.00

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.

3670 GLN   ( 811-)  E    4.67
1477 GLU   (  40-)  C    4.35

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.

2962 PRO   (  88-)  E    -3.0
  88 PRO   (  88-)  A    -3.0
1525 PRO   (  88-)  C    -3.0
5141 ARG   ( 845-)  G    -3.0
4399 PRO   (  88-)  G    -2.9
3704 ARG   ( 845-)  E    -2.9
 375 THR   ( 375-)  A    -2.8
1689 PRO   ( 252-)  C    -2.8
1107 ARG   (  50-)  B    -2.8
4686 THR   ( 375-)  G    -2.7
2373 GLU   ( 951-)  C    -2.7
 202 LYS   ( 202-)  A    -2.7
3981 ARG   (  50-)  F    -2.7
2852 PRO   ( 358-)  D    -2.7
5247 GLU   ( 951-)  G    -2.6
1414 SER   ( 357-)  B    -2.6
 936 GLU   ( 951-)  A    -2.6
 830 ARG   ( 845-)  A    -2.6
 571 ARG   ( 571-)  A    -2.6
1639 LYS   ( 202-)  C    -2.6
4870 ARG   ( 559-)  G    -2.6
5708 ILE   ( 340-)  H    -2.6
2851 SER   ( 357-)  D    -2.6
5039 ARG   ( 735-)  G    -2.6
 652 ARG   ( 652-)  A    -2.6
And so on for a total of 213 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
 329 GLY   ( 329-)  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
 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
 686 LYS   ( 686-)  A  Poor phi/psi
 710 TYR   ( 710-)  A  PRO omega poor
 781 LEU   ( 796-)  A  PRO omega poor
 785 THR   ( 800-)  A  Poor phi/psi
 806 GLN   ( 821-)  A  Poor phi/psi
 829 PRO   ( 844-)  A  Poor phi/psi
 845 PRO   ( 860-)  A  Poor phi/psi
 865 THR   ( 880-)  A  Poor phi/psi
And so on for a total of 153 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 : -4.055

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.

3713 SER   ( 854-)  E    0.36
4579 SER   ( 268-)  G    0.36
 312 SER   ( 312-)  A    0.36
1341 VAL   ( 284-)  B    0.36
4619 SER   ( 308-)  G    0.36
5468 SER   ( 100-)  H    0.36
1705 SER   ( 268-)  C    0.37
2594 SER   ( 100-)  D    0.37
 268 SER   ( 268-)  A    0.37
4030 SER   (  99-)  F    0.37
2778 VAL   ( 284-)  D    0.38
3142 SER   ( 268-)  E    0.38
1156 SER   (  99-)  B    0.39
3268 SER   ( 394-)  E    0.39
4888 GLU   ( 577-)  G    0.39
5150 SER   ( 854-)  G    0.40

Warning: Unusual backbone conformations

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

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

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

   3 LYS   (   3-)  A      0
   7 ILE   (   7-)  A      0
   9 SER   (   9-)  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
  81 GLU   (  81-)  A      0
  82 ARG   (  82-)  A      0
  83 PRO   (  83-)  A      0
  89 THR   (  89-)  A      0
  90 MET   (  90-)  A      0
  93 GLN   (  93-)  A      0
 107 VAL   ( 107-)  A      0
 116 ILE   ( 116-)  A      0
 139 ILE   ( 139-)  A      0
 146 SER   ( 146-)  A      0
 149 ALA   ( 149-)  A      0
And so on for a total of 1997 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 : 2.091

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!

2004 GLY   ( 567-)  C   3.20   24
4878 GLY   ( 567-)  G   3.18   22
 567 GLY   ( 567-)  A   3.15   19
3441 GLY   ( 567-)  E   3.10   32
5020 GLY   ( 709-)  G   2.29   14
3583 GLY   ( 709-)  E   1.94   16

Warning: Unusual peptide bond conformations

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

5054 ASP   ( 758-)  G   1.58

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    0.05 LOW
  17 PRO   (  17-)  A    0.13 LOW
  58 PRO   (  58-)  A    0.12 LOW
  68 PRO   (  68-)  A    0.12 LOW
  83 PRO   (  83-)  A    0.10 LOW
 290 PRO   ( 290-)  A    0.10 LOW
 360 PRO   ( 360-)  A    0.15 LOW
 411 PRO   ( 411-)  A    0.08 LOW
 418 PRO   ( 418-)  A    0.20 LOW
 524 PRO   ( 524-)  A    0.09 LOW
 555 PRO   ( 555-)  A    0.00 LOW
 620 PRO   ( 620-)  A    0.15 LOW
 647 PRO   ( 647-)  A    0.16 LOW
 666 PRO   ( 666-)  A    0.19 LOW
 690 PRO   ( 690-)  A    0.15 LOW
 711 PRO   ( 711-)  A    0.16 LOW
 716 PRO   ( 716-)  A    0.00 LOW
 782 PRO   ( 797-)  A    0.11 LOW
 829 PRO   ( 844-)  A    0.19 LOW
 836 PRO   ( 851-)  A    0.13 LOW
 871 PRO   ( 886-)  A    0.13 LOW
 886 PRO   ( 901-)  A    0.03 LOW
 890 PRO   ( 905-)  A    0.13 LOW
 973 PRO   ( 988-)  A    0.19 LOW
1115 PRO   (  58-)  B    0.05 LOW
And so on for a total of 152 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].

  88 PRO   (  88-)  A   -40.1 envelop C-alpha (-36 degrees)
 165 PRO   ( 165-)  A   -22.4 half-chair C-alpha/N (-18 degrees)
 200 PRO   ( 200-)  A   122.5 half-chair C-beta/C-alpha (126 degrees)
 302 PRO   ( 302-)  A   -45.8 half-chair C-beta/C-alpha (-54 degrees)
 318 PRO   ( 318-)  A   -65.1 envelop C-beta (-72 degrees)
 345 PRO   ( 345-)  A   -58.7 half-chair C-beta/C-alpha (-54 degrees)
 350 PRO   ( 350-)  A   112.5 envelop C-beta (108 degrees)
 635 PRO   ( 635-)  A   -43.9 envelop C-alpha (-36 degrees)
 870 PRO   ( 885-)  A    38.0 envelop C-delta (36 degrees)
 894 PRO   ( 909-)  A   -44.5 envelop C-alpha (-36 degrees)
 984 PRO   ( 999-)  A   142.2 envelop C-alpha (144 degrees)
1239 PRO   ( 182-)  B   -63.9 envelop C-beta (-72 degrees)
1304 PRO   ( 247-)  B   -45.7 half-chair C-beta/C-alpha (-54 degrees)
1353 PRO   ( 296-)  B   -62.4 half-chair C-beta/C-alpha (-54 degrees)
1415 PRO   ( 358-)  B   -42.5 envelop C-alpha (-36 degrees)
1525 PRO   (  88-)  C   -38.2 envelop C-alpha (-36 degrees)
1739 PRO   ( 302-)  C   -61.8 half-chair C-beta/C-alpha (-54 degrees)
1755 PRO   ( 318-)  C   -58.4 half-chair C-beta/C-alpha (-54 degrees)
1782 PRO   ( 345-)  C   -42.1 envelop C-alpha (-36 degrees)
1787 PRO   ( 350-)  C   103.3 envelop C-beta (108 degrees)
2103 PRO   ( 666-)  C   139.1 envelop C-alpha (144 degrees)
2308 PRO   ( 886-)  C   -60.9 half-chair C-beta/C-alpha (-54 degrees)
2323 PRO   ( 901-)  C   102.0 envelop C-beta (108 degrees)
2714 PRO   ( 220-)  D   125.1 half-chair C-beta/C-alpha (126 degrees)
2736 PRO   ( 242-)  D   -64.8 envelop C-beta (-72 degrees)
2852 PRO   ( 358-)  D   -41.0 envelop C-alpha (-36 degrees)
2891 PRO   (  17-)  E  -141.2 envelop C-delta (-144 degrees)
2962 PRO   (  88-)  E   -37.3 envelop C-alpha (-36 degrees)
3176 PRO   ( 302-)  E   -38.8 envelop C-alpha (-36 degrees)
3219 PRO   ( 345-)  E   -44.5 envelop C-alpha (-36 degrees)
3477 PRO   ( 603-)  E   -62.8 half-chair C-beta/C-alpha (-54 degrees)
3540 PRO   ( 666-)  E   111.6 envelop C-beta (108 degrees)
3703 PRO   ( 844-)  E    -1.2 envelop N (0 degrees)
3755 PRO   ( 896-)  E   -60.9 half-chair C-beta/C-alpha (-54 degrees)
3768 PRO   ( 909-)  E   -51.8 half-chair C-beta/C-alpha (-54 degrees)
4113 PRO   ( 182-)  F   -56.1 half-chair C-beta/C-alpha (-54 degrees)
4151 PRO   ( 220-)  F   133.7 half-chair C-beta/C-alpha (126 degrees)
4227 PRO   ( 296-)  F   -54.1 half-chair C-beta/C-alpha (-54 degrees)
4285 PRO   ( 354-)  F    45.2 half-chair C-delta/C-gamma (54 degrees)
4289 PRO   ( 358-)  F   -36.5 envelop C-alpha (-36 degrees)
4399 PRO   (  88-)  G   -46.6 half-chair C-beta/C-alpha (-54 degrees)
4476 PRO   ( 165-)  G   -53.6 half-chair C-beta/C-alpha (-54 degrees)
4481 PRO   ( 170-)  G    52.4 half-chair C-delta/C-gamma (54 degrees)
4511 PRO   ( 200-)  G   109.4 envelop C-beta (108 degrees)
4613 PRO   ( 302-)  G   -45.7 half-chair C-beta/C-alpha (-54 degrees)
4656 PRO   ( 345-)  G   -51.1 half-chair C-beta/C-alpha (-54 degrees)
4977 PRO   ( 666-)  G   141.8 envelop C-alpha (144 degrees)
5722 PRO   ( 354-)  H    99.5 envelop C-beta (108 degrees)
5726 PRO   ( 358-)  H   -33.3 envelop C-alpha (-36 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.

2306 ILE   ( 884-)  C      N   <-> 5850 HOH   (1743 )  C      O      0.59    2.11  INTRA BF
 960 HIS   ( 975-)  A      ND1 <-> 5271 HIS   ( 975-)  G      ND1    0.57    2.43  INTRA BL
1326 CYG   ( 269-)  B      N1  <-> 5849 HOH   (5022 )  B      O      0.53    2.17  INTRA
2397 HIS   ( 975-)  C      ND1 <-> 3834 HIS   ( 975-)  E      ND1    0.52    2.48  INTRA
2917 ARG   (  43-)  E      NH1 <-> 5852 HOH   (5867 )  E      O      0.46    2.24  INTRA BF
5419 GLN   (  51-)  H      NE2 <-> 5855 HOH   (3241 )  H      O      0.45    2.25  INTRA BL
4786 LYS   ( 475-)  G      NZ  <-> 5854 HOH   (5514 )  G      O      0.43    2.27  INTRA
3291 ASP   ( 417-)  E      OD2 <-> 3297 LYS   ( 423-)  E      NZ     0.43    2.27  INTRA BF
4354 ARG   (  43-)  G      NH2 <-> 4392 GLU   (  81-)  G      OE1    0.43    2.27  INTRA BF
 806 GLN   ( 821-)  A      NE2 <-> 5848 HOH   (5857 )  A      O      0.42    2.28  INTRA BF
1996 ARG   ( 559-)  C      NH2 <-> 5850 HOH   (1994 )  C      O      0.42    2.28  INTRA BF
4535 LYS   ( 224-)  G      NZ  <-> 5854 HOH   (5173 )  G      O      0.42    2.28  INTRA BF
2875 MET   (   1-)  E      N   <-> 5852 HOH   (5387 )  E      O      0.42    2.28  INTRA BF
2716 GLN   ( 222-)  D      NE2 <-> 5851 HOH   (1815 )  D      O      0.42    2.28  INTRA
3920 LYS   (1061-)  E    A NZ  <-> 5852 HOH   (5637 )  E      O      0.41    2.29  INTRA
5571 ARG   ( 203-)  H      NH1 <-> 5855 HOH   (4109 )  H      O      0.41    2.29  INTRA
  38 ARG   (  38-)  A      NH2 <-> 5848 HOH   (5735 )  A      O      0.41    2.29  INTRA BF
 224 LYS   ( 224-)  A      NZ  <-> 5848 HOH   (5169 )  A      O      0.41    2.29  INTRA BF
3433 ARG   ( 559-)  E      NH1 <-> 5852 HOH   (5798 )  E      O      0.41    2.29  INTRA BF
1442 THR   (   5-)  C      N   <-> 5850 HOH   (1167 )  C      O      0.41    2.29  INTRA
5446 GLN   (  78-)  H      NE2 <-> 5855 HOH   (3934 )  H      O      0.41    2.29  INTRA BF
5012 ALA   ( 701-)  G      O   <-> 5016 ALA   ( 705-)  G      N      0.41    2.29  INTRA BF
2328 LEU   ( 906-)  C      O   <-> 2334 ARG   ( 912-)  C      NH2    0.41    2.29  INTRA BF
5202 LEU   ( 906-)  G      O   <-> 5208 ARG   ( 912-)  G      NH2    0.41    2.29  INTRA BF
 799 GLN   ( 814-)  A      NE2 <-> 5848 HOH   (5628 )  A      O      0.41    2.29  INTRA BL
And so on for a total of 1511 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      -7.57
3857 ARG   ( 998-)  E      -7.38
3217 ARG   ( 343-)  E      -7.36
 343 ARG   ( 343-)  A      -7.24
2420 ARG   ( 998-)  C      -7.22
1780 ARG   ( 343-)  C      -6.97
 983 ARG   ( 998-)  A      -6.83
4654 ARG   ( 343-)  G      -6.82
2344 ARG   ( 922-)  C      -6.68
1620 TYR   ( 183-)  C      -6.39
5291 HIS   ( 995-)  G      -6.31
3854 HIS   ( 995-)  E      -6.31
3781 ARG   ( 922-)  E      -6.28
3057 TYR   ( 183-)  E      -6.26
 907 ARG   ( 922-)  A      -6.23
 183 TYR   ( 183-)  A      -6.20
4494 TYR   ( 183-)  G      -6.15
 174 MET   ( 174-)  A      -6.07
3048 MET   ( 174-)  E      -5.98
2306 ILE   ( 884-)  C      -5.92
4485 MET   ( 174-)  G      -5.91
5180 ILE   ( 884-)  G      -5.89
 869 ILE   ( 884-)  A      -5.85
1611 MET   ( 174-)  C      -5.83
1093 MET   (  36-)  B      -5.78
And so on for a total of 66 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.

 415 LEU   ( 415-)  A   -2.95
4334 ALA   (  23-)  G   -2.89
4550 ALA   ( 239-)  G   -2.85
4716 GLY   ( 405-)  G   -2.82
  60 MET   (  60-)  A   -2.80
1460 ALA   (  23-)  C   -2.78
3279 GLY   ( 405-)  E   -2.77
  61 ALA   (  61-)  A   -2.76
3752 VAL   ( 893-)  E   -2.76
 878 VAL   ( 893-)  A   -2.74
  23 ALA   (  23-)  A   -2.72
5189 VAL   ( 893-)  G   -2.71
3758 LYS   ( 899-)  E   -2.68
1842 GLY   ( 405-)  C   -2.66
2315 VAL   ( 893-)  C   -2.66
2321 LYS   ( 899-)  C   -2.63
 819 ASN   ( 834-)  A   -2.62
 940 GLU   ( 955-)  A   -2.56
1209 GLY   ( 152-)  B   -2.54
4083 GLY   ( 152-)  F   -2.54
 632 ILE   ( 632-)  A   -2.52
3704 ARG   ( 845-)  E   -2.52
5520 GLY   ( 152-)  H   -2.52

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        -1.78
1142 LEU   (  85-)  B     - 1145 ILE   (  88-)  B        -1.51
2012 GLY   ( 575-)  C     - 2015 PHE   ( 578-)  C        -1.81
2314 GLU   ( 892-)  C     - 2317 LEU   ( 895-)  C        -1.88
2579 LEU   (  85-)  D     - 2582 ILE   (  88-)  D        -1.81
3449 GLY   ( 575-)  E     - 3452 PHE   ( 578-)  E        -1.74
3751 GLU   ( 892-)  E     - 3754 LEU   ( 895-)  E        -1.85
4886 GLY   ( 575-)  G     - 4889 PHE   ( 578-)  G        -1.77
5453 LEU   (  85-)  H     - 5456 ILE   (  88-)  H        -1.82

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.

5848 HOH   (5695 )  A      O     25.79   -8.36  -83.50
5848 HOH   (5701 )  A      O     27.85   -7.39  -82.27
5848 HOH   (5766 )  A      O     -7.64   96.30   89.71
5848 HOH   (5774 )  A      O     -0.52  107.06   77.61
5848 HOH   (5789 )  A      O     -7.21  101.20   77.08
5848 HOH   (5790 )  A      O     -5.53  102.49   75.86
5848 HOH   (5864 )  A      O     -5.60   49.13  -47.34
5848 HOH   (5866 )  A      O     -5.17   51.45  -50.90
5848 HOH   (5902 )  A      O     28.97   -5.30  -81.79
5849 HOH   (5128 )  B      O     25.46  -49.68  -67.79
5850 HOH   (1254 )  C      O     63.18   35.63   47.01
5850 HOH   (1898 )  C      O     66.77   46.61   67.10
5850 HOH   (1899 )  C      O     64.41   43.89   66.75
5850 HOH   (1961 )  C      O    -25.99   71.37   49.91
5851 HOH   (2047 )  D      O     50.17   61.45   77.39

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.

5848 HOH   (5344 )  A      O
5848 HOH   (5711 )  A      O
5848 HOH   (5724 )  A      O
5848 HOH   (5729 )  A      O
5850 HOH   (1166 )  C      O
5850 HOH   (1226 )  C      O
5850 HOH   (1546 )  C      O
5850 HOH   (1982 )  C      O
5851 HOH   (1839 )  D      O
5851 HOH   (2055 )  D      O
5852 HOH   (5325 )  E      O
5852 HOH   (5498 )  E      O
5852 HOH   (5567 )  E      O
5852 HOH   (5882 )  E      O
5853 HOH   (3211 )  F      O
5854 HOH   (5722 )  G      O
5854 HOH   (5801 )  G      O
5855 HOH   (3902 )  H      O
Marked this atom as acceptor 5760  CL  (5011-) A     CL
Marked this atom as acceptor 5761  CL  (5012-) A     CL
Marked this atom as acceptor 5762  CL  (5013-) A     CL
Marked this atom as acceptor 5763  CL  (5014-) A     CL
Marked this atom as acceptor 5764  CL  (5015-) A     CL
Marked this atom as acceptor 5765  CL  (5018-) A     CL
Marked this atom as acceptor 5773  CL  (5016-) B     CL
Marked this atom as acceptor 5774  CL  (5017-) B     CL
Marked this atom as acceptor 5783  CL  (5035-) C     CL
Marked this atom as acceptor 5784  CL  (5036-) C     CL
Marked this atom as acceptor 5785  CL  (5037-) C     CL
Marked this atom as acceptor 5786  CL  (5038-) C     CL
Marked this atom as acceptor 5787  CL  (5039-) C     CL
Marked this atom as acceptor 5796  CL  (5040-) D     CL
Marked this atom as acceptor 5797  CL  (5041-) D     CL
Marked this atom as acceptor 5799  CL  (5058-) E     CL
Marked this atom as acceptor 5800  CL  (5059-) E     CL
Marked this atom as acceptor 5801  CL  (5060-) E     CL
Marked this atom as acceptor 5802  CL  (5061-) E     CL
Marked this atom as acceptor 5803  CL  (5062-) E     CL
Marked this atom as acceptor 5821  CL  (5063-) F     CL
Marked this atom as acceptor 5822  CL  (5064-) F     CL
Marked this atom as acceptor 5834  CL  (5083-) G     CL
Marked this atom as acceptor 5835  CL  (5084-) G     CL
Marked this atom as acceptor 5836  CL  (5085-) G     CL
Marked this atom as acceptor 5837  CL  (5086-) G     CL
Marked this atom as acceptor 5838  CL  (5087-) G     CL
Marked this atom as acceptor 5842  CL  (5088-) H     CL
Marked this atom as acceptor 5843  CL  (5089-) 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
Strange metal coordination for HIS 5384
ERROR. No convergence in HB2STD
Old,New value: 7225.853 7225.874
ERROR. No convergence in HB2STD
Old,New value: 7225.595 7225.614
ERROR. No convergence in HB2STD
Old,New value: 7231.599 7231.610

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
 266 ASN   ( 266-)  A
 523 HIS   ( 523-)  A
 769 GLN   ( 784-)  A
 773 HIS   ( 788-)  A
 820 ASN   ( 835-)  A
 972 ASN   ( 987-)  A
 985 HIS   (1000-)  A
1108 GLN   (  51-)  B
1116 HIS   (  59-)  B
1135 GLN   (  78-)  B
1408 GLN   ( 351-)  B
1542 GLN   ( 105-)  C
1680 HIS   ( 243-)  C
1703 ASN   ( 266-)  C
1991 ASN   ( 554-)  C
2007 ASN   ( 570-)  C
2206 GLN   ( 784-)  C
2257 ASN   ( 835-)  C
2409 ASN   ( 987-)  C
2424 GLN   (1002-)  C
2568 GLN   (  74-)  D
2572 GLN   (  78-)  D
2716 GLN   ( 222-)  D
2845 GLN   ( 351-)  D
2944 HIS   (  70-)  E
2979 GLN   ( 105-)  E
3024 HIS   ( 150-)  E
3140 ASN   ( 266-)  E
3428 ASN   ( 554-)  E
3643 GLN   ( 784-)  E
3693 ASN   ( 834-)  E
3859 HIS   (1000-)  E
3866 ASN   (1007-)  E
4282 GLN   ( 351-)  F
4381 HIS   (  70-)  G
4416 GLN   ( 105-)  G
4461 HIS   ( 150-)  G
4565 GLN   ( 254-)  G
4577 ASN   ( 266-)  G
5080 GLN   ( 784-)  G
5084 HIS   ( 788-)  G
5131 ASN   ( 835-)  G
5288 ASN   ( 992-)  G
5331 GLN   (1035-)  G
5473 HIS   ( 105-)  H
5590 GLN   ( 222-)  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
  49 SER   (  49-)  A      N
  72 GLU   (  72-)  A      N
  82 ARG   (  82-)  A      NE
 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
 249 THR   ( 249-)  A      OG1
 279 THR   ( 279-)  A      N
 285 GLN   ( 285-)  A      NE2
 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
 410 ASP   ( 410-)  A      N
 534 ALA   ( 534-)  A      N
 544 TYR   ( 544-)  A      OH
 556 SER   ( 556-)  A    A OG
 601 CYS   ( 601-)  A      N
And so on for a total of 267 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.

 236 ASN   ( 236-)  A      OD1
 391 GLN   ( 391-)  A      OE1
 746 GLU   ( 761-)  A      OE1
 746 GLU   ( 761-)  A      OE2
1108 GLN   (  51-)  B      OE1
1330 GLN   ( 273-)  B      OE1
1652 GLU   ( 215-)  C      OE1
1673 ASN   ( 236-)  C      OD1
1828 GLN   ( 391-)  C      OE1
1960 HIS   ( 523-)  C      ND1
2110 GLU   ( 673-)  C      OE2
2183 GLU   ( 761-)  C      OE2
2767 GLN   ( 273-)  D      OE1
3110 ASN   ( 236-)  E      OD1
3208 GLU   ( 334-)  E      OE1
3265 GLN   ( 391-)  E      OE1
3397 HIS   ( 523-)  E      ND1
3547 GLU   ( 673-)  E      OE2
3612 ASP   ( 753-)  E      OD1
3620 GLU   ( 761-)  E      OE2
4204 GLN   ( 273-)  F      OE1
4284 HIS   ( 353-)  F      NE2
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
5365 HIS   (1069-)  G      ND1
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+.

5753  MN   (5001-)  A   -.-  -.-  Part of ionic cluster
5754  MN   (5002-)  A   -.-  -.-  Part of ionic cluster
5756   K   (5004-)  A   -.-  -.-  Part of ionic cluster
5756   K   (5004-)  A     2.45   0.80 Could be NA
5757  MN   (5007-)  A   -.-  -.-  Part of ionic cluster
5758   K   (5008-)  A   -.-  -.-  Part of ionic cluster
5758   K   (5008-)  A   -.-  -.-  Too few ligands (2)
5767   K   (5021-)  A   -.-  -.-  Part of ionic cluster
5767   K   (5021-)  A   -.-  -.-  Too few ligands (3)
5768   K   (5022-)  A   -.-  -.-  Too few ligands (1)
5775   K   (5020-)  B   -.-  -.-  Too few ligands (3)
5776  MN   (5024-)  C   -.-  -.-  Part of ionic cluster
5777  MN   (5025-)  C   -.-  -.-  Part of ionic cluster
5779   K   (5027-)  C   -.-  -.-  Part of ionic cluster
5780  MN   (5030-)  C   -.-  -.-  Part of ionic cluster
5781   K   (5031-)  C   -.-  -.-  Part of ionic cluster
5788   K   (5042-)  C   -.-  -.-  Too few ligands (3)
5789   K   (5044-)  C   -.-  -.-  Part of ionic cluster
5789   K   (5044-)  C    0.70  -.-   Poor packing
5805   K   (5067-)  E   -.-  -.-  Part of ionic cluster
5805   K   (5067-)  E   -.-  -.-  Too few ligands (3)
5806   K   (5068-)  E   -.-  -.-  Too few ligands (0)
5807   K   (5069-)  E   -.-  -.-  Too few ligands (2)
5808  MN   (5047-)  E   -.-  -.-  Part of ionic cluster
5809  MN   (5048-)  E   -.-  -.-  Part of ionic cluster
5810   K   (5049-)  E     1.56   0.73 Scores about as good as NA
5811   K   (5050-)  E   -.-  -.-  Part of ionic cluster
5812  MN   (5053-)  E   -.-  -.-  Part of ionic cluster
5813   K   (5054-)  E   -.-  -.-  Part of ionic cluster
5813   K   (5054-)  E   -.-  -.-  Too few ligands (2)
5823   K   (5066-)  F    0.73  -.-   Poor packing (Few ligands (4) )
5825   K   (5092-)  G   -.-  -.-  Part of ionic cluster
5827  MN   (5072-)  G   -.-  -.-  Part of ionic cluster
5828  MN   (5073-)  G   -.-  -.-  Part of ionic cluster
5829   K   (5074-)  G     1.78   0.74 Scores about as good as NA
5830   K   (5075-)  G   -.-  -.-  Part of ionic cluster
5831  MN   (5078-)  G   -.-  -.-  Part of ionic cluster
5832   K   (5079-)  G   -.-  -.-  Part of ionic cluster
5832   K   (5079-)  G   -.-  -.-  Too few ligands (3)
5841   K   (5091-)  H   -.-  -.-  Too few ligands (2)

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.

5848 HOH   (5184 )  A      O  0.93  K  4 *1
5848 HOH   (5366 )  A      O  1.10  K  4 *1
5850 HOH   (1153 )  C      O  0.89  K  4 *1 NCS 2/2
5850 HOH   (1435 )  C      O  1.04  K  4 *1 NCS 2/2
5852 HOH   (5165 )  E      O  0.90  K  4 *1 NCS 2/2
5852 HOH   (5421 )  E      O  1.09  K  5 *1 NCS 1/1
5852 HOH   (5528 )  E      O  0.96  K  4 *1 NCS 2/2
5852 HOH   (5596 )  E      O  0.99  K  4 *1 NCS 2/2
5853 HOH   (2493 )  F      O  1.10  K  4 *1 NCS 2/2
5853 HOH   (3099 )  F      O  1.02  K  4 *1
5854 HOH   (5264 )  G      O  0.89 NA  4 H2O-B NCS 4/4
5854 HOH   (5384 )  G      O  1.12  K  4 *1 NCS 3/3
5854 HOH   (5460 )  G      O  1.01  K  4 *1 Ion-B NCS 3/3
5855 HOH   (3590 )  H      O  1.05  K  4 *1 NCS 3/3

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.

 334 GLU   ( 334-)  A   H-bonding suggests Gln; but Alt-Rotamer
 410 ASP   ( 410-)  A   H-bonding suggests Asn
 430 ASP   ( 430-)  A   H-bonding suggests Asn; but Alt-Rotamer
 518 ASP   ( 518-)  A   H-bonding suggests Asn
 754 ASP   ( 769-)  A   H-bonding suggests Asn; but Alt-Rotamer
 776 ASP   ( 791-)  A   H-bonding suggests Asn
 792 ASP   ( 807-)  A   H-bonding suggests Asn
1009 GLU   (1024-)  A   H-bonding suggests Gln
1010 ASP   (1025-)  A   H-bonding suggests Asn
1026 ASP   (1041-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1098 GLU   (  41-)  B   H-bonding suggests Gln; but Alt-Rotamer
1169 ASP   ( 112-)  B   H-bonding suggests Asn
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
2191 ASP   ( 769-)  C   H-bonding suggests Asn
2213 ASP   ( 791-)  C   H-bonding suggests Asn
2446 GLU   (1024-)  C   H-bonding suggests Gln
2463 ASP   (1041-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
2606 ASP   ( 112-)  D   H-bonding suggests Asn
2705 ASP   ( 211-)  D   H-bonding suggests Asn; but Alt-Rotamer
3208 GLU   ( 334-)  E   H-bonding suggests Gln
3392 ASP   ( 518-)  E   H-bonding suggests Asn
3628 ASP   ( 769-)  E   H-bonding suggests Asn
3650 ASP   ( 791-)  E   H-bonding suggests Asn; but Alt-Rotamer
4043 ASP   ( 112-)  F   H-bonding suggests Asn
4645 GLU   ( 334-)  G   H-bonding suggests Gln; but Alt-Rotamer
4721 ASP   ( 410-)  G   H-bonding suggests Asn; but Alt-Rotamer
4741 ASP   ( 430-)  G   H-bonding suggests Asn; but Alt-Rotamer
4829 ASP   ( 518-)  G   H-bonding suggests Asn
4994 GLU   ( 683-)  G   H-bonding suggests Gln
5049 ASP   ( 753-)  G   H-bonding suggests Asn
5065 ASP   ( 769-)  G   H-bonding suggests Asn
5087 ASP   ( 791-)  G   H-bonding suggests Asn; but Alt-Rotamer
5103 ASP   ( 807-)  G   H-bonding suggests Asn; but Alt-Rotamer
5320 GLU   (1024-)  G   H-bonding suggests Gln
5321 ASP   (1025-)  G   H-bonding suggests Asn
5337 ASP   (1041-)  G   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
5480 ASP   ( 112-)  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 :   0.249
  2nd generation packing quality :  -1.178
  Ramachandran plot appearance   :  -1.366
  chi-1/chi-2 rotamer normality  :  -4.055 (bad)
  Backbone conformation          :   0.238

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.880
  Bond angles                    :   1.210
  Omega angle restraints         :   0.380 (tight)
  Side chain planarity           :   0.879
  Improper dihedral distribution :   1.326
  B-factor distribution          :   3.893 (loose)
  Inside/Outside distribution    :   1.013

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.880
  Bond angles                    :   1.210
  Omega angle restraints         :   0.380 (tight)
  Side chain planarity           :   0.879
  Improper dihedral distribution :   1.326
  B-factor distribution          :   3.893 (loose)
  Inside/Outside distribution    :   1.013
==============

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,
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