WHAT IF Check report

This file was created 2012-01-05 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 pdb1o1e.ent

Checks that need to be done early-on in validation

Warning: Class of space group could be incorrect

The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file.

Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly.

Crystal class of the cell: CUBIC

Crystal class of the space group: TRICLINIC

Space group name: P 1

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 7.645
CA-only RMS fit for the two chains : 7.638

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 12.388
CA-only RMS fit for the two chains : 12.421

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: A and J

All-atom RMS fit for the two chains : 17.252
CA-only RMS fit for the two chains : 17.301

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 J

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 M

All-atom RMS fit for the two chains : 12.624
CA-only RMS fit for the two chains : 12.655

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 M

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 P

All-atom RMS fit for the two chains : 13.157
CA-only RMS fit for the two chains : 13.190

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 P

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 1309237.9
Volume of the Unit Cell V= 27008100.0
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 20.629
Vm by authors and this calculated Vm do not agree very well

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 212 GLN   ( 215-)  A  -
 405 VAL   ( 408-)  A  -
 406 GLY   ( 409-)  A  -
 408 GLU   ( 411-)  A  -
 503 GLU   ( 506-)  A  -
 534 GLU   ( 537-)  A  -
 540 PRO   ( 543-)  A  -
 626 GLU   ( 629-)  A  -
 629 GLY   ( 632-)  A  -
 630 GLY   ( 633-)  A  -
 634 LYS   ( 637-)  A  -
 635 GLY   ( 638-)  A  -
 729 ILE   ( 732-)  A  -
 733 GLN   ( 736-)  A  -
 754 GLN   ( 757-)  A  -
 758 GLY   ( 761-)  A  -
 759 HIS   ( 762-)  A  -
 933 SER   ( 111-)  B  -
 949 ARG   ( 127-)  B  -
 959 TRP   ( 137-)  B  -
 987 LYS   (   4-)  C  -
1026 ASN   (  43-)  C  -
1344 GLN   ( 215-)  D  -
1537 VAL   ( 408-)  D  -
1538 GLY   ( 409-)  D  -
And so on for a total of 168 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Note: Ramachandran plot

Chain identifier: 9

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

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.

  16 MLY   (  19-)  A  -
  27 MLY   (  30-)  A  -
  32 MLY   (  35-)  A  -
  46 MLY   (  49-)  A  -
  52 MLY   (  55-)  A  -
  56 MLY   (  59-)  A  -
  60 MLY   (  63-)  A  -
  81 MLY   (  84-)  A  -
  84 MLY   (  87-)  A  -
 104 MLY   ( 107-)  A  -
 127 MLY   ( 130-)  A  -
 135 MLY   ( 138-)  A  -
 187 MLY   ( 190-)  A  -
 233 MLY   ( 236-)  A  -
 245 MLY   ( 248-)  A  -
 269 MLY   ( 272-)  A  -
 292 MLY   ( 295-)  A  -
 293 MLY   ( 296-)  A  -
 344 MLY   ( 348-)  A  -
 349 MLY   ( 353-)  A  -
 363 MLY   ( 367-)  A  -
 365 MLY   ( 369-)  A  -
 381 MLY   ( 385-)  A  -
 411 MLY   ( 415-)  A  -
 427 MLY   ( 431-)  A  -
And so on for a total of 266 lines.

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:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.000

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: B

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: C

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: D

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: E

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: F

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: G

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: H

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: I

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: J

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: K

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: L

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: M

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: N

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: O

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: P

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Q

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: R

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 1

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 2

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 3

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 4

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 5

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 6

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 7

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 8

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 9

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: V

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: W

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: X

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Y

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Z

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 982 ARG   (  19-)  C  -
 998 ARG   (  35-)  C  -
1055 ARG   (  92-)  C  -
1071 ARG   ( 108-)  C  -
2096 ARG   (  19-)  F  -
2112 ARG   (  35-)  F  -
2168 ARG   (  92-)  F  -
2184 ARG   ( 108-)  F  -
3212 ARG   (  19-)  I  -
3228 ARG   (  35-)  I  -
3285 ARG   (  92-)  I  -
3301 ARG   ( 108-)  I  -
4325 ARG   (  19-)  L  -
4341 ARG   (  35-)  L  -
4398 ARG   (  92-)  L  -
4414 ARG   ( 108-)  L  -
5439 ARG   (  19-)  O  -
5455 ARG   (  35-)  O  -
5511 ARG   (  92-)  O  -
5527 ARG   ( 108-)  O  -
6555 ARG   (  19-)  R  -
6571 ARG   (  35-)  R  -
6626 ARG   (  92-)  R  -
6642 ARG   ( 108-)  R  -

Warning: Tyrosine convention problem

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

 953 TYR   ( 150-)  B  -
1102 TYR   ( 139-)  C  -
2067 TYR   ( 150-)  E  -
2214 TYR   ( 139-)  F  -
3183 TYR   ( 150-)  H  -
3332 TYR   ( 139-)  I  -
4296 TYR   ( 150-)  K  -
4445 TYR   ( 139-)  L  -
5410 TYR   ( 150-)  N  -
5558 TYR   ( 139-)  O  -
6526 TYR   ( 150-)  Q  -
6673 TYR   ( 139-)  R  -

Warning: Phenylalanine convention problem

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

 836 PHE   (  31-)  B  -
 885 PHE   (  80-)  B  -
 906 PHE   ( 101-)  B  -
 921 PHE   ( 116-)  B  -
 945 PHE   ( 140-)  B  -
 977 PHE   (  14-)  C  -
 980 PHE   (  17-)  C  -
1028 PHE   (  65-)  C  -
1050 PHE   (  87-)  C  -
1057 PHE   (  94-)  C  -
1951 PHE   (  31-)  E  -
2000 PHE   (  80-)  E  -
2021 PHE   ( 101-)  E  -
2035 PHE   ( 116-)  E  -
2058 PHE   ( 140-)  E  -
2091 PHE   (  14-)  F  -
2094 PHE   (  17-)  F  -
2141 PHE   (  65-)  F  -
2163 PHE   (  87-)  F  -
2170 PHE   (  94-)  F  -
3066 PHE   (  31-)  H  -
3115 PHE   (  80-)  H  -
3136 PHE   ( 101-)  H  -
3151 PHE   ( 116-)  H  -
3175 PHE   ( 140-)  H  -
And so on for a total of 60 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.

 825 ASP   (  20-)  B  -
 831 ASP   (  26-)  B  -
 850 ASP   (  45-)  B  -
 851 ASP   (  46-)  B  -
 900 ASP   (  95-)  B  -
 952 ASP   ( 149-)  B  -
 965 ASP   ( 162-)  B  -
 971 ASP   (   8-)  C  -
 995 ASP   (  32-)  C  -
1049 ASP   (  86-)  C  -
1058 ASP   (  95-)  C  -
1940 ASP   (  20-)  E  -
1946 ASP   (  26-)  E  -
1965 ASP   (  45-)  E  -
1966 ASP   (  46-)  E  -
2015 ASP   (  95-)  E  -
2066 ASP   ( 149-)  E  -
2079 ASP   ( 162-)  E  -
2085 ASP   (   8-)  F  -
2109 ASP   (  32-)  F  -
2162 ASP   (  86-)  F  -
2171 ASP   (  95-)  F  -
3055 ASP   (  20-)  H  -
3061 ASP   (  26-)  H  -
3080 ASP   (  45-)  H  -
And so on for a total of 65 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.

 828 GLU   (  23-)  B  -
 830 GLU   (  25-)  B  -
 834 GLU   (  29-)  B  -
 854 GLU   (  49-)  B  -
 875 GLU   (  70-)  B  -
 891 GLU   (  86-)  B  -
 975 GLU   (  12-)  C  -
1030 GLU   (  67-)  C  -
1048 GLU   (  85-)  C  -
1052 GLU   (  89-)  C  -
1069 GLU   ( 106-)  C  -
1079 GLU   ( 116-)  C  -
1083 GLU   ( 120-)  C  -
1084 GLU   ( 121-)  C  -
1094 GLU   ( 131-)  C  -
1943 GLU   (  23-)  E  -
1945 GLU   (  25-)  E  -
1949 GLU   (  29-)  E  -
1969 GLU   (  49-)  E  -
1990 GLU   (  70-)  E  -
2006 GLU   (  86-)  E  -
2089 GLU   (  12-)  F  -
2143 GLU   (  67-)  F  -
2161 GLU   (  85-)  F  -
2165 GLU   (  89-)  F  -
And so on for a total of 90 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.

   1 ASP   (   4-)  A  -   CG   OD1   1.33    4.4
  20 GLU   (  23-)  A  -   CD   OE1   1.33    4.3
  23 GLU   (  26-)  A  -   CD   OE1   1.33    4.1
  65 GLU   (  68-)  A  -   CD   OE2   1.33    4.1
  72 ASP   (  75-)  A  -   CG   OD1   1.34    4.8
  83 ASP   (  86-)  A  -   CG   OD1   1.34    4.5
  95 HIS   (  98-)  A  -   CB   CG    1.44   -4.4
 105 GLU   ( 108-)  A  -   CD   OE1   1.34    4.7
 199 SER   ( 202-)  A  -   CB   OG    1.52    5.0
 199 SER   ( 202-)  A  -   N   -C     1.24   -4.2
 215 LEU   ( 218-)  A  -   CB   CG    1.69    7.8
 216 GLU   ( 219-)  A  -   N   -C     1.21   -5.8
 238 ASP   ( 241-)  A  -   CG   OD1   1.34    4.6
 285 PHE   ( 288-)  A  -   CA   C     1.44   -4.2
 303 THR   ( 306-)  A  -   CB   OG1   1.36   -4.5
 324 ASP   ( 327-)  A  -   CG   OD1   1.33    4.3
 327 GLU   ( 330-)  A  -   CD   OE1   1.33    4.1
 342 ASP   ( 346-)  A  -   CG   OD2   1.33    4.5
 343 GLU   ( 347-)  A  -   CD   OE1   1.33    4.4
 372 GLU   ( 376-)  A  -   CD   OE1   1.33    4.2
 377 GLU   ( 381-)  A  -   CD   OE1   1.34    4.8
 407 GLU   ( 411-)  A  -   CD   OE1   1.34    4.8
 430 TYR   ( 434-)  A  -   CA   CB    1.44   -4.5
 472 GLU   ( 476-)  A  -   CD   OE1   1.35    5.2
 493 VAL   ( 497-)  A  -   N   -C     1.24   -4.2
And so on for a total of 412 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

 |  1.002574  0.000083 -0.000015|
 |  0.000083  1.002419  0.000123|
 | -0.000015  0.000123  1.001544|
Proposed new scale matrix

 |  0.003324  0.000000  0.000000|
 |  0.000000  0.003325  0.000000|
 |  0.000000  0.000000  0.003328|
With corresponding cell

    A    = 300.802  B   = 300.756  C    = 300.493
    Alpha=  90.003  Beta=  90.003  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 300.000  B   = 300.000  C    = 300.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1812.472
(Under-)estimated Z-score: 31.376

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.

  19 LYS   (  22-)  A  -   C    CA   CB  118.55    4.4
  35 VAL   (  38-)  A  -   N    CA   CB  102.70   -4.6
  44 PHE   (  47-)  A  -   C    CA   CB  100.95   -4.8
  68 THR   (  71-)  A  -   N    CA   CB  117.36    4.0
  72 ASP   (  75-)  A  -   N    CA   CB  122.97    7.3
  79 PRO   (  82-)  A  -   N    CA   CB  109.32    5.7
  85 ILE   (  88-)  A  -   CB   CG1  CD1 101.52   -5.8
  95 HIS   (  98-)  A  -   C    CA   CB   87.33  -12.0
  95 HIS   (  98-)  A  -   CD2  CG   ND1 110.37    4.3
 101 TYR   ( 104-)  A  -   C    CA   CB  117.86    4.1
 115 TYR   ( 118-)  A  -   C    CA   CB  101.44   -4.6
 125 PRO   ( 128-)  A  -   N    CA   CB  108.16    4.7
 134 PRO   ( 137-)  A  -  -CA  -C    N   108.54   -5.6
 138 LEU   ( 141-)  A  -   C    CA   CB   97.86   -6.4
 158 ASN   ( 161-)  A  -   CA   CB   CG  107.66   -4.9
 158 ASN   ( 161-)  A  -   ND2  CG   OD1 127.32    4.7
 162 PHE   ( 165-)  A  -   N    CA   CB  100.32   -6.0
 162 PHE   ( 165-)  A  -   CA   CB   CG  108.85   -5.0
 169 ASN   ( 172-)  A  -   N    CA   CB  118.14    4.5
 170 GLN   ( 173-)  A  -   N    CA   CB  102.97   -4.4
 177 GLU   ( 180-)  A  -   N    CA   CB  118.53    4.7
 189 VAL   ( 192-)  A  -   CA   CB   CG1 101.91   -5.1
 193 PHE   ( 196-)  A  -   CA   CB   CG  108.27   -5.5
 199 SER   ( 202-)  A  -   C    CA   CB   95.34   -7.8
 211 MET   ( 214-)  A  -   CG   SD   CE  110.09    4.2
And so on for a total of 3085 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.

 825 ASP   (  20-)  B  -
 828 GLU   (  23-)  B  -
 830 GLU   (  25-)  B  -
 831 ASP   (  26-)  B  -
 834 GLU   (  29-)  B  -
 850 ASP   (  45-)  B  -
 851 ASP   (  46-)  B  -
 854 GLU   (  49-)  B  -
 875 GLU   (  70-)  B  -
 891 GLU   (  86-)  B  -
 900 ASP   (  95-)  B  -
 952 ASP   ( 149-)  B  -
 965 ASP   ( 162-)  B  -
 971 ASP   (   8-)  C  -
 975 GLU   (  12-)  C  -
 982 ARG   (  19-)  C  -
 995 ASP   (  32-)  C  -
 998 ARG   (  35-)  C  -
1030 GLU   (  67-)  C  -
1048 GLU   (  85-)  C  -
1049 ASP   (  86-)  C  -
1052 GLU   (  89-)  C  -
1055 ARG   (  92-)  C  -
1058 ASP   (  95-)  C  -
1069 GLU   ( 106-)  C  -
And so on for a total of 179 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.

  72 ASP   (  75-)  A  -   CA   -12.3     9.28    33.73
  95 HIS   (  98-)  A  -   CA     8.3    49.44    34.11
  95 HIS   (  98-)  A  -   C      8.6    12.98     0.15
 134 PRO   ( 137-)  A  -   N      6.1    17.59    -2.48
 261 ASP   ( 264-)  A  -   CA     7.8    49.24    33.73
 337 LEU   ( 341-)  A  -   CA    -8.6    21.09    34.19
 443 GLN   ( 447-)  A  -   CA   -12.3    10.26    33.96
 476 ILE   ( 480-)  A  -   CB     6.6    40.84    32.31
 615 THR   ( 625-)  A  -   CB     6.5    48.68    34.09
 618 GLY   ( 628-)  A  -   C     -6.2    -8.11     0.06
 626 LYS   ( 637-)  A  -   C    -17.5   -26.32     0.11
 634 THR   ( 648-)  A  -   CB   -13.6     3.53    34.09
 635 VAL   ( 649-)  A  -   C      7.9    10.95     0.15
 635 VAL   ( 649-)  A  -   CB   -35.1   -78.99   -32.96
 684 ASN   ( 698-)  A  -   C     -6.1    -9.24     0.27
 740 THR   ( 756-)  A  -   CA     6.6    44.83    33.84
 745 HIS   ( 762-)  A  -   CA    -7.2    20.89    34.11
 812 MET   ( 832-)  A  -   CA    -7.5    20.59    34.17
 820 PRO   ( 840-)  A  -   N     -6.2   -22.72    -2.48
 826 GLU   (  21-)  B  -   C      6.6     9.47    -0.03
 827 THR   (  22-)  B  -   C      7.5    11.49     0.30
 829 ILE   (  24-)  B  -   C      6.4     8.39     0.03
 849 LYS   (  44-)  B  -   C      6.0     9.19     0.11
 850 ASP   (  45-)  B  -   C      6.3     9.64    -0.01
 857 ALA   (  52-)  B  -   C      6.2     9.58     0.08
And so on for a total of 315 lines.

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.

1179  ARG  ( 335-) Z  -   7.41
1069  ARG  ( 335-) W  -   7.41
8867 ARG   ( 335-)  6  -   7.40
8124 ARG   ( 335-)  4  -   7.39
8496 ARG   ( 335-)  5  -   7.38
7383 ARG   ( 335-)  2  -   7.37
1142  ARG  ( 335-) Y  -   7.36
1105  ARG  ( 335-) X  -   7.36
7012 ARG   ( 335-)  1  -   7.36
7752 ARG   ( 335-)  3  -   7.35
9238 ARG   ( 335-)  7  -   7.35
4108 ALA   ( 784-)  J  -   6.65
5222 ALA   ( 784-)  M  -   6.64
6337 ALA   ( 784-)  P  -   6.61
1879 ALA   ( 784-)  D  -   6.61
 766 ALA   ( 784-)  A  -   6.60
2994 ALA   ( 784-)  G  -   6.56
4671 GLU   ( 219-)  M  -   6.29
3558 GLU   ( 219-)  J  -   6.27
2439 GLU   ( 219-)  G  -   6.27
5783 GLU   ( 219-)  P  -   6.26
 216 GLU   ( 219-)  A  -   6.22
1328 GLU   ( 219-)  D  -   6.22
1145  ALA  ( 365-) Y  -   6.09
7041 ALA   ( 365-)  1  -   6.09
And so on for a total of 291 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.671

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.

5410 TYR   ( 150-)  N  -  15.63
3183 TYR   ( 150-)  H  -  15.63
 953 TYR   ( 150-)  B  -  15.55
6526 TYR   ( 150-)  Q  -  15.41
2067 TYR   ( 150-)  E  -  15.34
4296 TYR   ( 150-)  K  -  15.10
4324 ASP   (  18-)  L  -   9.79
6554 ASP   (  18-)  R  -   9.74
5438 ASP   (  18-)  O  -   9.73
2095 ASP   (  18-)  F  -   9.73
3211 ASP   (  18-)  I  -   9.65
 981 ASP   (  18-)  C  -   9.60
2027 ASP   ( 107-)  E  -   8.36
4255 ASP   ( 107-)  K  -   8.25
6485 ASP   ( 107-)  Q  -   8.21
 912 ASP   ( 107-)  B  -   8.18
5369 ASP   ( 107-)  N  -   8.16
3142 ASP   ( 107-)  H  -   8.11
6623 GLU   (  89-)  R  -   7.04
5508 GLU   (  89-)  O  -   7.02
4395 GLU   (  89-)  L  -   7.02
3282 GLU   (  89-)  I  -   6.87
2165 GLU   (  89-)  F  -   6.81
1052 GLU   (  89-)  C  -   6.81
5421 GLU   ( 161-)  N  -   5.83
And so on for a total of 110 lines.

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

6182 PHE   ( 623-)  P  -   CB   7.02
3959 PHE   ( 623-)  J  -   CB   7.01
1727 PHE   ( 623-)  D  -   CB   7.01
 613 PHE   ( 623-)  A  -   CB   7.00
5069 PHE   ( 623-)  M  -   CB   6.99
2843 PHE   ( 623-)  G  -   CB   6.98
1146  HIS  ( 371-) Y  -    CB   5.62
1000  HIS  ( 371-) 9  -    CB   5.61
7788 HIS   ( 371-)  3  -   CB   5.60
1036  HIS  ( 371-) V  -    CB   5.60
9637 HIS   ( 371-)  8  -   CB   5.60
7419 HIS   ( 371-)  2  -   CB   5.59
8903 HIS   ( 371-)  6  -   CB   5.59
1109  HIS  ( 371-) X  -    CB   5.59
1183  HIS  ( 371-) Z  -    CB   5.58
8160 HIS   ( 371-)  4  -   CB   5.58
7047 HIS   ( 371-)  1  -   CB   5.58
1072  HIS  ( 371-) W  -    CB   5.57
8532 HIS   ( 371-)  5  -   CB   5.57
9274 HIS   ( 371-)  7  -   CB   5.56
1053  HIS  ( 173-) W  -    CB   4.22
7592 HIS   ( 173-)  3  -   CB   4.19
7221 HIS   ( 173-)  2  -   CB   4.19
1163  HIS  ( 173-) Z  -    CB   4.18
1090  HIS  ( 173-) X  -    CB   4.18
6852 HIS   ( 173-)  1  -   CB   4.18
1017  HIS  ( 173-) V  -    CB   4.17
8706 HIS   ( 173-)  6  -   CB   4.17
8334 HIS   ( 173-)  5  -   CB   4.17
9444 HIS   ( 173-)  8  -   CB   4.16
1126  HIS  ( 173-) Y  -    CB   4.16
9808 HIS   ( 173-)  9  -   CB   4.16
9077 HIS   ( 173-)  7  -   CB   4.16
7962 HIS   ( 173-)  4  -   CB   4.14
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.486

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.486

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.

2059 PRO   ( 141-)  E  -   -2.9
3176 PRO   ( 141-)  H  -   -2.9
 946 PRO   ( 141-)  B  -   -2.9
4288 PRO   ( 141-)  K  -   -2.9
6518 PRO   ( 141-)  Q  -   -2.9
5402 PRO   ( 141-)  N  -   -2.9
5267 PRO   ( 830-)  M  -   -2.9
1925 PRO   ( 830-)  D  -   -2.9
 810 PRO   ( 830-)  A  -   -2.9
4153 PRO   ( 830-)  J  -   -2.9
3040 PRO   ( 830-)  G  -   -2.9
6383 PRO   ( 830-)  P  -   -2.9
5225 ILE   ( 787-)  M  -   -2.9
6340 ILE   ( 787-)  P  -   -2.9
2350 TYR   ( 129-)  G  -   -2.8
4581 TYR   ( 129-)  M  -   -2.8
1238 TYR   ( 129-)  D  -   -2.8
5694 TYR   ( 129-)  P  -   -2.8
3468 TYR   ( 129-)  J  -   -2.8
 126 TYR   ( 129-)  A  -   -2.8
7898 PRO   ( 109-)  4  -   -2.8
1083  PRO  ( 109-) X  -   -2.8
1011  PRO  ( 109-) V  -   -2.8
9382 PRO   ( 109-)  8  -   -2.8
8642 PRO   ( 109-)  6  -   -2.8
And so on for a total of 658 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.

   8 GLY   (  11-)  A  - Poor phi/psi
  18 GLU   (  21-)  A  - Poor phi/psi
  55 GLY   (  58-)  A  - Poor phi/psi
  70 LYS   (  73-)  A  - Poor phi/psi
 110 TRP   ( 113-)  A  - Poor phi/psi
 126 TYR   ( 129-)  A  - Poor phi/psi
 134 PRO   ( 137-)  A  - Poor phi/psi
 167 ARG   ( 170-)  A  - Poor phi/psi
 196 ILE   ( 199-)  A  - Poor phi/psi
 198 ALA   ( 201-)  A  - Poor phi/psi
 199 SER   ( 202-)  A  - Poor phi/psi
 201 GLU   ( 204-)  A  - Poor phi/psi
 208 SER   ( 211-)  A  - Poor phi/psi
 210 LYS   ( 213-)  A  - Poor phi/psi
 216 GLU   ( 219-)  A  - Poor phi/psi
 291 ASN   ( 294-)  A  - Poor phi/psi
 301 LEU   ( 304-)  A  - Poor phi/psi
 367 ARG   ( 371-)  A  - Poor phi/psi
 407 GLU   ( 411-)  A  - Poor phi/psi
 501 GLY   ( 507-)  A  - Poor phi/psi
 550 GLY   ( 560-)  A  - Poor phi/psi
 562 LYS   ( 572-)  A  - Poor phi/psi
 567 ALA   ( 577-)  A  - omega poor
 635 VAL   ( 649-)  A  - omega poor
 636 SER   ( 650-)  A  - Poor phi/psi
And so on for a total of 415 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 : -4.611

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.

 333 SER   ( 336-)  A  -   0.33
1445 SER   ( 336-)  D  -   0.33
2556 SER   ( 336-)  G  -   0.33
3675 SER   ( 336-)  J  -   0.33
 156 SER   ( 159-)  A  -   0.36
1268 SER   ( 159-)  D  -   0.36
2380 SER   ( 159-)  G  -   0.36
3498 SER   ( 159-)  J  -   0.36
4611 SER   ( 159-)  M  -   0.36
5724 SER   ( 159-)  P  -   0.36
 416 SER   ( 420-)  A  -   0.37
1527 SER   ( 420-)  D  -   0.37
2640 SER   ( 420-)  G  -   0.37
3756 SER   ( 420-)  J  -   0.37
4868 SER   ( 420-)  M  -   0.37
5981 SER   ( 420-)  P  -   0.37
6958 SER   ( 281-)  1  -   0.40
7329 SER   ( 281-)  2  -   0.40
7700 SER   ( 281-)  3  -   0.40
8070 SER   ( 281-)  4  -   0.40
8442 SER   ( 281-)  5  -   0.40
8813 SER   ( 281-)  6  -   0.40
9185 SER   ( 281-)  7  -   0.40
9552 SER   ( 281-)  8  -   0.40
9915 SER   ( 281-)  9  -   0.40
1028  SER  ( 281-) V  -   0.40
1064  SER  ( 281-) W  -   0.40
1100  SER  ( 281-) X  -   0.40
1137  SER  ( 281-) Y  -   0.40
1174  SER  ( 281-) Z  -   0.40
ERROR. Too many residues to use DSSP

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!

   4 MET   (   7-)  A  -     0
   7 PHE   (  10-)  A  -     0
  14 LEU   (  17-)  A  -     0
  15 ARG   (  18-)  A  -     0
  16 MLY   (  19-)  A  -     0
  27 MLY   (  30-)  A  -     0
  28 PRO   (  31-)  A  -     0
  32 MLY   (  35-)  A  -     0
  33 SER   (  36-)  A  -     0
  34 SER   (  37-)  A  -     0
  42 GLN   (  45-)  A  -     0
  43 SER   (  46-)  A  -     0
  44 PHE   (  47-)  A  -     0
  46 MLY   (  49-)  A  -     0
  52 MLY   (  55-)  A  -     0
  53 GLU   (  56-)  A  -     0
  56 MLY   (  59-)  A  -     0
  60 MLY   (  63-)  A  -     0
  62 GLU   (  65-)  A  -     0
  65 GLU   (  68-)  A  -     0
  72 ASP   (  75-)  A  -     0
  73 GLN   (  76-)  A  -     0
  81 MLY   (  84-)  A  -     0
  83 ASP   (  86-)  A  -     0
  84 MLY   (  87-)  A  -     0
And so on for a total of 4638 lines.

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!

2288 GLY   (  67-)  G  -  2.50   80
  64 GLY   (  67-)  A  -  2.50   80
3406 GLY   (  67-)  J  -  2.50   80
1176 GLY   (  67-)  D  -  2.50   80
4519 GLY   (  67-)  M  -  2.50   80
5632 GLY   (  67-)  P  -  2.49   80
2749 PRO   ( 529-)  G  -  2.29   11
 523 PRO   ( 529-)  A  -  2.29   11
1636 PRO   ( 529-)  D  -  2.29   11
3865 PRO   ( 529-)  J  -  2.29   11
4977 PRO   ( 529-)  M  -  2.29   11
6090 PRO   ( 529-)  P  -  2.29   11
5844 PRO   ( 280-)  P  -  2.20   10
2500 PRO   ( 280-)  G  -  2.20   10
1389 PRO   ( 280-)  D  -  2.20   10
4732 PRO   ( 280-)  M  -  2.20   10
3619 PRO   ( 280-)  J  -  2.20   10
 277 PRO   ( 280-)  A  -  2.20   10
 403 GLY   ( 407-)  A  -  2.04   15
1515 GLY   ( 407-)  D  -  2.03   16
2627 GLY   ( 407-)  G  -  2.03   16
6192 GLY   ( 635-)  P  -  1.94   10
7194 GLY   ( 146-)  2  -  1.59   80
7935 GLY   ( 146-)  4  -  1.59   80
1087  GLY  ( 146-) X  -  1.58   80
9050 GLY   ( 146-)  7  -  1.58   80
8307 GLY   ( 146-)  5  -  1.58   80
8679 GLY   ( 146-)  6  -  1.58   80
7565 GLY   ( 146-)  3  -  1.58   80
1124  GLY  ( 146-) Y  -  1.58   80

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]

  12 PRO   (  15-)  A  -   0.04 LOW
  28 PRO   (  31-)  A  -   0.09 LOW
  40 PRO   (  43-)  A  -   0.10 LOW
  79 PRO   (  82-)  A  -   0.15 LOW
  80 PRO   (  83-)  A  -   0.12 LOW
  97 PRO   ( 100-)  A  -   0.20 LOW
 125 PRO   ( 128-)  A  -   0.07 LOW
 130 PRO   ( 133-)  A  -   0.15 LOW
 134 PRO   ( 137-)  A  -   0.18 LOW
 149 PRO   ( 152-)  A  -   0.20 LOW
 224 PRO   ( 227-)  A  -   0.04 LOW
 277 PRO   ( 280-)  A  -   0.11 LOW
 294 PRO   ( 297-)  A  -   0.08 LOW
 306 PRO   ( 309-)  A  -   0.20 LOW
 320 PRO   ( 323-)  A  -   0.14 LOW
 373 PRO   ( 377-)  A  -   0.08 LOW
 400 PRO   ( 404-)  A  -   0.15 LOW
 450 PRO   ( 454-)  A  -   0.02 LOW
 523 PRO   ( 529-)  A  -   0.13 LOW
 536 PRO   ( 543-)  A  -   0.06 LOW
 558 PRO   ( 568-)  A  -   0.02 LOW
 560 PRO   ( 570-)  A  -   0.07 LOW
 592 PRO   ( 602-)  A  -   0.03 LOW
 655 PRO   ( 669-)  A  -   0.13 LOW
 663 PRO   ( 677-)  A  -   0.02 LOW
And so on for a total of 286 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].

 150 PRO   ( 153-)  A  -  171.5 envelop N (180 degrees)
 810 PRO   ( 830-)  A  -  156.5 half-chair C-alpha/N (162 degrees)
 946 PRO   ( 141-)  B  - -160.1 half-chair N/C-delta (-162 degrees)
1004 PRO   (  41-)  C  -  -10.5 half-chair C-alpha/N (-18 degrees)
1262 PRO   ( 153-)  D  -  171.4 envelop N (180 degrees)
1925 PRO   ( 830-)  D  -  156.5 half-chair C-alpha/N (162 degrees)
2059 PRO   ( 141-)  E  - -160.3 half-chair N/C-delta (-162 degrees)
2118 PRO   (  41-)  F  -  -10.7 half-chair C-alpha/N (-18 degrees)
2374 PRO   ( 153-)  G  -  171.7 envelop N (180 degrees)
3040 PRO   ( 830-)  G  -  156.8 half-chair C-alpha/N (162 degrees)
3176 PRO   ( 141-)  H  - -159.6 half-chair N/C-delta (-162 degrees)
3234 PRO   (  41-)  I  -  -10.9 half-chair C-alpha/N (-18 degrees)
3492 PRO   ( 153-)  J  -  171.7 envelop N (180 degrees)
4153 PRO   ( 830-)  J  -  156.7 half-chair C-alpha/N (162 degrees)
4288 PRO   ( 141-)  K  - -160.3 half-chair N/C-delta (-162 degrees)
4347 PRO   (  41-)  L  -  -10.5 half-chair C-alpha/N (-18 degrees)
4605 PRO   ( 153-)  M  -  171.5 envelop N (180 degrees)
5267 PRO   ( 830-)  M  -  156.5 half-chair C-alpha/N (162 degrees)
5402 PRO   ( 141-)  N  - -160.2 half-chair N/C-delta (-162 degrees)
5461 PRO   (  41-)  O  -  -10.4 half-chair C-alpha/N (-18 degrees)
5718 PRO   ( 153-)  P  -  171.4 envelop N (180 degrees)
6383 PRO   ( 830-)  P  -  156.8 half-chair C-alpha/N (162 degrees)
6518 PRO   ( 141-)  Q  - -160.3 half-chair N/C-delta (-162 degrees)
6577 PRO   (  41-)  R  -  -10.6 half-chair C-alpha/N (-18 degrees)
6790 PRO   ( 109-)  1  -  112.3 envelop C-beta (108 degrees)
7157 PRO   ( 109-)  2  -  112.3 envelop C-beta (108 degrees)
7528 PRO   ( 109-)  3  -  112.3 envelop C-beta (108 degrees)
7898 PRO   ( 109-)  4  -  112.3 envelop C-beta (108 degrees)
8270 PRO   ( 109-)  5  -  112.3 envelop C-beta (108 degrees)
8642 PRO   ( 109-)  6  -  112.3 envelop C-beta (108 degrees)
9013 PRO   ( 109-)  7  -  112.4 envelop C-beta (108 degrees)
9382 PRO   ( 109-)  8  -  112.2 envelop C-beta (108 degrees)
9745 PRO   ( 109-)  9  -  112.3 envelop C-beta (108 degrees)
1011  PRO  ( 109-) V  -  112.3 envelop C-beta (108 degrees)
1047  PRO  ( 109-) W  -  112.4 envelop C-beta (108 degrees)
1083  PRO  ( 109-) X  -  112.3 envelop C-beta (108 degrees)
1120  PRO  ( 109-) Y  -  112.3 envelop C-beta (108 degrees)
1157  PRO  ( 109-) Z  -  112.4 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

2040 LEU   ( 121-)  E  -   CD1  <->  2046 PHE   ( 128-)  E  -   CD2  2.62    0.58  INTRA
3156 LEU   ( 121-)  H  -   CD1  <->  3163 PHE   ( 128-)  H  -   CD2  2.62    0.58  INTRA
 926 LEU   ( 121-)  B  -   CD1  <->   933 PHE   ( 128-)  B  -   CD2  2.62    0.58  INTRA
6498 LEU   ( 121-)  Q  -   CD1  <->  6505 PHE   ( 128-)  Q  -   CD2  2.62    0.58  INTRA
5382 LEU   ( 121-)  N  -   CD1  <->  5389 PHE   ( 128-)  N  -   CD2  2.62    0.58  INTRA
4269 LEU   ( 121-)  K  -   CD1  <->  4276 PHE   ( 128-)  K  -   CD2  2.62    0.58  INTRA
2857 LYS   ( 642-)  G  -   CE   <->  1034  SER  ( 344-) V  -    CB   2.46    0.74  INTRA
1741 LYS   ( 642-)  D  -   CE   <->  9977 SER   ( 344-)  9  -   CB   2.45    0.75  INTRA
6199 LYS   ( 642-)  P  -   CE   <->  7021 SER   ( 344-)  1  -   CB   2.45    0.75  INTRA
5084 LYS   ( 642-)  M  -   CE   <->  1180  SER  ( 344-) Z  -    CB   2.45    0.75  INTRA
5398 TRP   ( 137-)  N  -   CH2  <->  5406 GLY   ( 146-)  N  -   N    2.29    0.81  INTRA
6514 TRP   ( 137-)  Q  -   CH2  <->  6522 GLY   ( 146-)  Q  -   N    2.29    0.81  INTRA
2055 TRP   ( 137-)  E  -   CH2  <->  2063 GLY   ( 146-)  E  -   N    2.29    0.81  INTRA
 942 TRP   ( 137-)  B  -   CH2  <->   950 GLY   ( 146-)  B  -   N    2.29    0.81  INTRA
3172 TRP   ( 137-)  H  -   CH2  <->  3180 GLY   ( 146-)  H  -   N    2.29    0.81  INTRA
 795 PHE   ( 814-)  A  -   CE1  <->   932 ARG   ( 127-)  B  -   NH2  2.28    0.82  INTRA
5080 LYS   ( 637-)  M  -   C    <->  1180  ILE  ( 345-) Z  -    CD1  2.21    0.99  INTRA
1735 GLY   ( 632-)  D  -   C    <->  9661 ASP   (  25-)  9  -   N    2.19    0.91  INTRA
2725 MLY   ( 505-)  G  -   CH2  <->  2973 HIS   ( 762-)  G  -   CE1  2.18    1.02  INTRA
2370 GLN   ( 149-)  G  -   OE1  <->  2974 THR   ( 763-)  G  -   CG2  2.15    0.65  INTRA
1324 GLN   ( 215-)  D  -   CD   <->  1448 ILE   ( 340-)  D  -   N    2.12    0.98  INTRA
3554 GLN   ( 215-)  J  -   CD   <->  3678 ILE   ( 340-)  J  -   N    2.12    0.98  INTRA
4667 GLN   ( 215-)  M  -   CD   <->  4791 ILE   ( 340-)  M  -   N    2.12    0.98  INTRA
 212 GLN   ( 215-)  A  -   CD   <->   336 ILE   ( 340-)  A  -   N    2.11    0.99  INTRA
1658 MLY   ( 553-)  D  -   CH2  <->  1041  VAL  (  45-) W  -    CG2  2.09    1.11  INTRA
And so on for a total of 8451 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

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.

 982 ARG   (  19-)  C  -     -7.74
4325 ARG   (  19-)  L  -     -7.72
3212 ARG   (  19-)  I  -     -7.71
5439 ARG   (  19-)  O  -     -7.70
6555 ARG   (  19-)  R  -     -7.66
2096 ARG   (  19-)  F  -     -7.53
8574 GLN   (  41-)  6  -     -7.51
1150  GLN  (  41-) Z  -     -7.51
1077  GLN  (  41-) X  -     -7.51
8945 GLN   (  41-)  7  -     -7.51
7830 GLN   (  41-)  4  -     -7.51
9314 GLN   (  41-)  8  -     -7.51
9677 GLN   (  41-)  9  -     -7.51
6722 GLN   (  41-)  1  -     -7.51
1040  GLN  (  41-) W  -     -7.51
1113  GLN  (  41-) Y  -     -7.50
8202 GLN   (  41-)  5  -     -7.50
1004  GLN  (  41-) V  -     -7.50
5694 TYR   ( 129-)  P  -     -7.41
3468 TYR   ( 129-)  J  -     -7.41
 126 TYR   ( 129-)  A  -     -7.41
4581 TYR   ( 129-)  M  -     -7.40
2350 TYR   ( 129-)  G  -     -7.40
1238 TYR   ( 129-)  D  -     -7.40
1114  MET  (  44-) Y  -     -7.24
And so on for a total of 332 lines.

Warning: Abnormal packing environment for sequential residues

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

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

 566 GLU   ( 576-)  A  -    568 - HIS    578- ( A)  -      -4.28
1257 ARG   ( 148-)  D  -   1259 - GLU    150- ( D)  -      -4.78
1680 GLU   ( 576-)  D  -   1682 - HIS    578- ( D)  -      -4.28
2796 GLU   ( 576-)  G  -   2798 - HIS    578- ( G)  -      -4.26
2921 ARG   ( 708-)  G  -   2923 - GLY    710- ( G)  -      -4.57
3487 ARG   ( 148-)  J  -   3489 - GLU    150- ( J)  -      -4.67
3912 GLU   ( 576-)  J  -   3914 - HIS    578- ( J)  -      -4.26
4600 ARG   ( 148-)  M  -   4602 - GLU    150- ( M)  -      -4.73
5022 GLU   ( 576-)  M  -   5024 - HIS    578- ( M)  -      -4.27
5713 ARG   ( 148-)  P  -   5715 - GLU    150- ( P)  -      -4.73
6135 GLU   ( 576-)  P  -   6137 - HIS    578- ( P)  -      -4.27
6720 ARG   (  39-)  1  -   6722 - GLN     41- ( 1)  -      -6.72
7087 ARG   (  39-)  2  -   7089 - GLN     41- ( 2)  -      -5.88
7459 ARG   (  39-)  3  -   7461 - GLN     41- ( 3)  -      -5.68
7828 ARG   (  39-)  4  -   7830 - GLN     41- ( 4)  -      -6.73
8200 ARG   (  39-)  5  -   8202 - GLN     41- ( 5)  -      -6.72
8572 ARG   (  39-)  6  -   8574 - GLN     41- ( 6)  -      -6.73
8943 ARG   (  39-)  7  -   8945 - GLN     41- ( 7)  -      -6.73
9312 ARG   (  39-)  8  -   9314 - GLN     41- ( 8)  -      -6.71
9675 ARG   (  39-)  9  -   9677 - GLN     41- ( 9)  -      -6.73
1004  ARG  (  39-) V  -    1004 -  GLN    41- (V ) -       -6.71
1040  ARG  (  39-) W  -    1040 -  GLN    41- (W ) -       -6.71
1076  ARG  (  39-) X  -    1077 -  GLN    41- (X ) -       -6.75
1113  ARG  (  39-) Y  -    1113 -  GLN    41- (Y ) -       -6.73
1150  ARG  (  39-) Z  -    1150 -  GLN    41- (Z ) -       -6.57

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

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: M

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: N

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: O

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: P

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: Q

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: R

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: 1

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: 2

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: 3

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: 4

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: 5

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: 6

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: 7

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: 8

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: 9

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: V

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: W

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: X

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: Y

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: Z

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.

 969 ALA   (   6-)  C  -  -3.14
2083 ALA   (   6-)  F  -  -3.14
3199 ALA   (   6-)  I  -  -3.14
4564 ALA   ( 112-)  M  -  -2.88
 109 ALA   ( 112-)  A  -  -2.88
1221 ALA   ( 112-)  D  -  -2.88
5677 ALA   ( 112-)  P  -  -2.88
1120  PRO  ( 109-) Y  -  -2.85
1047  PRO  ( 109-) W  -  -2.85
7157 PRO   ( 109-)  2  -  -2.85
1011  PRO  ( 109-) V  -  -2.85
1157  PRO  ( 109-) Z  -  -2.85
1083  PRO  ( 109-) X  -  -2.85
6790 PRO   ( 109-)  1  -  -2.82
9337 ILE   (  64-)  8  -  -2.71
6266 GLY   ( 710-)  P  -  -2.68
5410 TYR   ( 150-)  N  -  -2.68
2067 TYR   ( 150-)  E  -  -2.68
6526 TYR   ( 150-)  Q  -  -2.67
1043  ILE  (  64-) W  -  -2.65
4840 LEU   ( 389-)  M  -  -2.62
5953 LEU   ( 389-)  P  -  -2.62
 385 LEU   ( 389-)  A  -  -2.62
3727 LEU   ( 389-)  J  -  -2.62
1497 LEU   ( 389-)  D  -  -2.61
2609 LEU   ( 389-)  G  -  -2.61
1571 ILE   ( 464-)  D  -  -2.61
3800 ILE   ( 464-)  J  -  -2.61
2684 ILE   ( 464-)  G  -  -2.61
 460 ILE   ( 464-)  A  -  -2.61
6025 ILE   ( 464-)  P  -  -2.61
4912 ILE   ( 464-)  M  -  -2.61
9495 GLU   ( 224-)  8  -  -2.59
3913 ALA   ( 577-)  J  -  -2.55
9700 ILE   (  64-)  9  -  -2.54
 146 GLN   ( 149-)  A  -  -2.52
8201 HIS   (  40-)  5  -  -2.51
1170  ASP  ( 244-) Z  -  -2.51
8480 ALA   ( 319-)  5  -  -2.51

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.

 585 TRP   ( 595-)  A  -  -  588 MLY   ( 598-)  A  -   -251.21
1699 TRP   ( 595-)  D  -  - 1702 MLY   ( 598-)  D  -   -251.21
1738 GLY   ( 639-)  D  -  - 1742 GLY   ( 643-)  D  -     -1.69
1935 PRO   ( 840-)  D  -  - 1938 LYS   ( 843-)  D  -     -1.97
2815 TRP   ( 595-)  G  -  - 2818 MLY   ( 598-)  G  -   -251.21
3050 PRO   ( 840-)  G  -  - 3053 LYS   ( 843-)  G  -     -2.04
3931 TRP   ( 595-)  J  -  - 3934 MLY   ( 598-)  J  -   -251.21
5041 TRP   ( 595-)  M  -  - 5044 MLY   ( 598-)  M  -   -251.21
5081 GLY   ( 639-)  M  -  - 5085 GLY   ( 643-)  M  -     -1.69
5277 PRO   ( 840-)  M  -  - 5280 LYS   ( 843-)  M  -     -1.94
6154 TRP   ( 595-)  P  -  - 6157 MLY   ( 598-)  P  -   -251.21
6197 LYS   ( 640-)  P  -  - 6200 GLY   ( 643-)  P  -     -2.01
6393 PRO   ( 840-)  P  -  - 6396 LYS   ( 843-)  P  -     -1.83
1182  ILE  ( 369-) Z  -   - 1183  ARG  ( 372-) Z  -      -1.72
ERROR. Too many residues to use DSSP

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: 8

Note: Second generation quality Z-score plot

Chain identifier: 9

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Water, ion, and hydrogenbond related checks

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.

  25 GLN   (  28-)  A  -
 124 ASN   ( 127-)  A  -
 477 ASN   ( 481-)  A  -
 581 ASN   ( 591-)  A  -
 644 ASN   ( 658-)  A  -
1236 ASN   ( 127-)  D  -
1588 ASN   ( 481-)  D  -
1695 ASN   ( 591-)  D  -
1756 ASN   ( 658-)  D  -
2348 ASN   ( 127-)  G  -
2701 ASN   ( 481-)  G  -
2811 ASN   ( 591-)  G  -
2871 ASN   ( 658-)  G  -
2973 HIS   ( 762-)  G  -
3466 ASN   ( 127-)  J  -
3817 ASN   ( 481-)  J  -
3927 ASN   ( 591-)  J  -
3987 ASN   ( 658-)  J  -
4017 HIS   ( 688-)  J  -
4050 GLN   ( 722-)  J  -
4140 GLN   ( 817-)  J  -
4579 ASN   ( 127-)  M  -
4929 ASN   ( 481-)  M  -
5037 ASN   ( 591-)  M  -
5099 ASN   ( 658-)  M  -
And so on for a total of 59 lines.

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.

   4 MET   (   7-)  A  -   N
   5 ALA   (   8-)  A  -   N
   7 PHE   (  10-)  A  -   N
   8 GLY   (  11-)  A  -   N
  22 ILE   (  25-)  A  -   N
  42 GLN   (  45-)  A  -   N
  44 PHE   (  47-)  A  -   N
  46 MLY   (  49-)  A  -   N
  56 MLY   (  59-)  A  -   N
  58 THR   (  61-)  A  -   N
  98 ALA   ( 101-)  A  -   N
 109 ALA   ( 112-)  A  -   N
 110 TRP   ( 113-)  A  -   NE1
 112 ILE   ( 115-)  A  -   N
 115 TYR   ( 118-)  A  -   OH
 119 PHE   ( 122-)  A  -   N
 120 CYS   ( 123-)  A  -   N
 122 THR   ( 125-)  A  -   OG1
 131 VAL   ( 134-)  A  -   N
 132 TYR   ( 135-)  A  -   N
 133 ASN   ( 136-)  A  -   N
 135 MLY   ( 138-)  A  -   N
 138 LEU   ( 141-)  A  -   N
 141 ARG   ( 144-)  A  -   NH1
 145 ARG   ( 148-)  A  -   NE
And so on for a total of 1721 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.

  83 ASP   (  86-)  A  -   OD2
  93 HIS   (  96-)  A  -   ND1
  95 HIS   (  98-)  A  -   ND1
 105 GLU   ( 108-)  A  -   OE2
 151 HIS   ( 154-)  A  -   ND1
 227 GLU   ( 230-)  A  -   OE2
 238 ASP   ( 241-)  A  -   OD1
 356 HIS   ( 360-)  A  -   ND1
 407 GLU   ( 411-)  A  -   OE1
 431 GLU   ( 435-)  A  -   OE1
 472 GLU   ( 476-)  A  -   OE2
 495 GLU   ( 499-)  A  -   OE1
 579 ASP   ( 589-)  A  -   OD2
 589 ASN   ( 599-)  A  -   OD1
 619 GLU   ( 629-)  A  -   OE1
 641 GLU   ( 655-)  A  -   OE2
 674 HIS   ( 688-)  A  -   ND1
 684 ASN   ( 698-)  A  -   OD1
 705 ASP   ( 719-)  A  -   OD1
 840 ASP   (  35-)  B  -   OD1
 841 GLN   (  36-)  B  -   OE1
 964 GLU   ( 161-)  B  -   OE1
1020 GLU   (  57-)  C  -   OE2
1058 ASP   (  95-)  C  -   OD2
1195 ASP   (  86-)  D  -   OD2
And so on for a total of 339 lines.

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 216 GLU   ( 219-)  A  -  H-bonding suggests Gln
 217 ASP   ( 220-)  A  -  H-bonding suggests Asn
 238 ASP   ( 241-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 314 GLU   ( 317-)  A  -  H-bonding suggests Gln
 380 ASP   ( 384-)  A  -  H-bonding suggests Asn
 532 GLU   ( 539-)  A  -  H-bonding suggests Gln
 595 GLU   ( 605-)  A  -  H-bonding suggests Gln
 705 ASP   ( 719-)  A  -  H-bonding suggests Asn
 736 ASP   ( 752-)  A  -  H-bonding suggests Asn
 789 GLU   ( 808-)  A  -  H-bonding suggests Gln
 830 GLU   (  25-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
 831 ASP   (  26-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 834 GLU   (  29-)  B  -  H-bonding suggests Gln
 840 ASP   (  35-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 854 GLU   (  49-)  B  -  H-bonding suggests Gln
 870 ASP   (  65-)  B  -  H-bonding suggests Asn
 891 GLU   (  86-)  B  -  H-bonding suggests Gln
 897 ASP   (  92-)  B  -  H-bonding suggests Asn
 910 ASP   ( 105-)  B  -  H-bonding suggests Asn
 924 GLU   ( 119-)  B  -  H-bonding suggests Gln
 952 ASP   ( 149-)  B  -  H-bonding suggests Asn
 975 GLU   (  12-)  C  -  H-bonding suggests Gln; but Alt-Rotamer
 981 ASP   (  18-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
1052 GLU   (  89-)  C  -  H-bonding suggests Gln; but Alt-Rotamer
1058 ASP   (  95-)  C  -  H-bonding suggests Asn
And so on for a total of 239 lines.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.865
  2nd generation packing quality :  -1.956
  Ramachandran plot appearance   :  -4.486 (bad)
  chi-1/chi-2 rotamer normality  :  -4.611 (bad)
  Backbone conformation          :  -1.021

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.963
  Bond angles                    :   1.537
  Omega angle restraints         :   0.752
  Side chain planarity           :   1.479
  Improper dihedral distribution :   1.875 (loose)
  B-factor distribution          :   0.363
  Inside/Outside distribution    :   1.012

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 : 70.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.963
  Bond angles                    :   1.537
  Omega angle restraints         :   0.752
  Side chain planarity           :   1.479
  Improper dihedral distribution :   1.875 (loose)
  B-factor distribution          :   0.363
  Inside/Outside distribution    :   1.012
==============

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.