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 pdb1o1a.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 : 7.605
CA-only RMS fit for the two chains : 7.598

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 : 12.424
CA-only RMS fit for the two chains : 12.457

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 : 17.241
CA-only RMS fit for the two chains : 17.291

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 : 5.630
CA-only RMS fit for the two chains : 5.554

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 : 13.820
CA-only RMS fit for the two chains : 13.863

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  -
 644 GLN   ( 647-)  A  -
 729 ILE   ( 732-)  A  -
 733 GLN   ( 736-)  A  -
 758 GLY   ( 761-)  A  -
 759 HIS   ( 762-)  A  -
 876 MET   (  54-)  B  -
 933 SER   ( 111-)  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 171 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.

 984 ARG   (  19-)  C  -
1000 ARG   (  35-)  C  -
1057 ARG   (  92-)  C  -
1073 ARG   ( 108-)  C  -
2096 ARG   (  19-)  F  -
2112 ARG   (  35-)  F  -
2168 ARG   (  92-)  F  -
2184 ARG   ( 108-)  F  -
3211 ARG   (  19-)  I  -
3227 ARG   (  35-)  I  -
3284 ARG   (  92-)  I  -
3300 ARG   ( 108-)  I  -
4323 ARG   (  19-)  L  -
4339 ARG   (  35-)  L  -
4396 ARG   (  92-)  L  -
4412 ARG   ( 108-)  L  -
5437 ARG   (  19-)  O  -
5453 ARG   (  35-)  O  -
5510 ARG   (  92-)  O  -
5526 ARG   ( 108-)  O  -
6553 ARG   (  19-)  R  -
6569 ARG   (  35-)  R  -
6625 ARG   (  92-)  R  -
6641 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

 955 TYR   ( 150-)  B  -
1104 TYR   ( 139-)  C  -
2067 TYR   ( 150-)  E  -
2214 TYR   ( 139-)  F  -
3182 TYR   ( 150-)  H  -
3331 TYR   ( 139-)  I  -
4294 TYR   ( 150-)  K  -
4443 TYR   ( 139-)  L  -
5408 TYR   ( 150-)  N  -
5557 TYR   ( 139-)  O  -
6524 TYR   ( 150-)  Q  -
6672 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.

 838 PHE   (  31-)  B  -
 887 PHE   (  80-)  B  -
 908 PHE   ( 101-)  B  -
 923 PHE   ( 116-)  B  -
 947 PHE   ( 140-)  B  -
 979 PHE   (  14-)  C  -
 982 PHE   (  17-)  C  -
1030 PHE   (  65-)  C  -
1052 PHE   (  87-)  C  -
1059 PHE   (  94-)  C  -
1952 PHE   (  31-)  E  -
2001 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  -
3065 PHE   (  31-)  H  -
3114 PHE   (  80-)  H  -
3135 PHE   ( 101-)  H  -
3150 PHE   ( 116-)  H  -
3174 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.

 827 ASP   (  20-)  B  -
 833 ASP   (  26-)  B  -
 852 ASP   (  45-)  B  -
 853 ASP   (  46-)  B  -
 902 ASP   (  95-)  B  -
 954 ASP   ( 149-)  B  -
 967 ASP   ( 162-)  B  -
 973 ASP   (   8-)  C  -
 997 ASP   (  32-)  C  -
1051 ASP   (  86-)  C  -
1060 ASP   (  95-)  C  -
1941 ASP   (  20-)  E  -
1947 ASP   (  26-)  E  -
1966 ASP   (  45-)  E  -
1967 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  -
3054 ASP   (  20-)  H  -
3060 ASP   (  26-)  H  -
3079 ASP   (  45-)  H  -
And so on for a total of 66 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.

 830 GLU   (  23-)  B  -
 832 GLU   (  25-)  B  -
 836 GLU   (  29-)  B  -
 856 GLU   (  49-)  B  -
 877 GLU   (  70-)  B  -
 893 GLU   (  86-)  B  -
 977 GLU   (  12-)  C  -
1032 GLU   (  67-)  C  -
1050 GLU   (  85-)  C  -
1054 GLU   (  89-)  C  -
1071 GLU   ( 106-)  C  -
1081 GLU   ( 116-)  C  -
1085 GLU   ( 120-)  C  -
1086 GLU   ( 121-)  C  -
1096 GLU   ( 131-)  C  -
1944 GLU   (  23-)  E  -
1946 GLU   (  25-)  E  -
1950 GLU   (  29-)  E  -
1970 GLU   (  49-)  E  -
1991 GLU   (  70-)  E  -
2007 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    4.2
  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    4.7
  95 HIS   (  98-)  A  -   CB   CG    1.44   -4.3
 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     1.25   -4.2
 214 THR   ( 217-)  A  -   CA   CB    1.61    4.0
 215 LEU   ( 218-)  A  -   CB   CG    1.69    7.8
 216 GLU   ( 219-)  A  -   N   -C     1.21   -5.7
 238 ASP   ( 241-)  A  -   CG   OD1   1.34    4.7
 263 GLU   ( 266-)  A  -   CD   OE2   1.33    4.0
 285 PHE   ( 288-)  A  -   CA   C     1.44   -4.2
 303 THR   ( 306-)  A  -   CB   OG1   1.36   -4.4
 324 ASP   ( 327-)  A  -   CG   OD1   1.33    4.4
 327 GLU   ( 330-)  A  -   CD   OE1   1.33    4.1
 342 ASP   ( 346-)  A  -   CG   OD2   1.34    4.6
 343 GLU   ( 347-)  A  -   CD   OE1   1.33    4.4
 372 GLU   ( 376-)  A  -   CD   OE1   1.33    4.1
 377 GLU   ( 381-)  A  -   CD   OE1   1.34    4.8
 407 GLU   ( 411-)  A  -   CD   OE1   1.34    4.9
 430 TYR   ( 434-)  A  -   CA   CB    1.44   -4.5
And so on for a total of 423 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

 |  1.001733  0.000051 -0.000334|
 |  0.000051  1.001655  0.000499|
 | -0.000334  0.000499  1.001654|
Proposed new scale matrix

 |  0.003327  0.000000  0.000001|
 |  0.000000  0.003327 -0.000002|
 |  0.000001 -0.000002  0.003327|
With corresponding cell

    A    = 300.550  B   = 300.527  C    = 300.526
    Alpha=  89.943  Beta=  90.038  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: 1096.972
(Under-)estimated Z-score: 24.410

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  118.59    4.5
  35 VAL   (  38-)  A  -   N    CA   CB  102.74   -4.6
  44 PHE   (  47-)  A  -   C    CA   CB  100.96   -4.8
  68 THR   (  71-)  A  -   N    CA   CB  117.35    4.0
  72 ASP   (  75-)  A  -   N    CA   CB  122.90    7.3
  72 ASP   (  75-)  A  -   C    CA   CB  117.72    4.0
  79 PRO   (  82-)  A  -   N    CA   CB  109.34    5.8
  85 ILE   (  88-)  A  -   CB   CG1  CD1 101.54   -5.8
  95 HIS   (  98-)  A  -   C    CA   CB   87.32  -12.0
  95 HIS   (  98-)  A  -   CD2  CG   ND1 110.39    4.3
 101 TYR   ( 104-)  A  -   C    CA   CB  117.89    4.1
 115 TYR   ( 118-)  A  -   C    CA   CB  101.43   -4.6
 125 PRO   ( 128-)  A  -   N    CA   CB  108.18    4.7
 134 PRO   ( 137-)  A  -  -CA  -C    N   108.41   -5.7
 138 LEU   ( 141-)  A  -   C    CA   CB   97.92   -6.4
 150 PRO   ( 153-)  A  -   N    CA   CB  107.46    4.1
 158 ASN   ( 161-)  A  -   CA   CB   CG  107.56   -5.0
 158 ASN   ( 161-)  A  -   ND2  CG   OD1 127.35    4.7
 162 PHE   ( 165-)  A  -   N    CA   CB  100.36   -6.0
 162 PHE   ( 165-)  A  -   CA   CB   CG  108.77   -5.0
 169 ASN   ( 172-)  A  -   N    CA   CB  118.18    4.5
 170 GLN   ( 173-)  A  -   N    CA   CB  103.00   -4.4
 177 GLU   ( 180-)  A  -   N    CA   CB  118.48    4.7
 189 VAL   ( 192-)  A  -   CA   CB   CG1 102.06   -5.0
 193 PHE   ( 196-)  A  -   CA   CB   CG  108.23   -5.6
And so on for a total of 3102 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.

 827 ASP   (  20-)  B  -
 830 GLU   (  23-)  B  -
 832 GLU   (  25-)  B  -
 833 ASP   (  26-)  B  -
 836 GLU   (  29-)  B  -
 852 ASP   (  45-)  B  -
 853 ASP   (  46-)  B  -
 856 GLU   (  49-)  B  -
 877 GLU   (  70-)  B  -
 893 GLU   (  86-)  B  -
 902 ASP   (  95-)  B  -
 954 ASP   ( 149-)  B  -
 967 ASP   ( 162-)  B  -
 973 ASP   (   8-)  C  -
 977 GLU   (  12-)  C  -
 984 ARG   (  19-)  C  -
 997 ASP   (  32-)  C  -
1000 ARG   (  35-)  C  -
1032 GLU   (  67-)  C  -
1050 GLU   (  85-)  C  -
1051 ASP   (  86-)  C  -
1054 GLU   (  89-)  C  -
1057 ARG   (  92-)  C  -
1060 ASP   (  95-)  C  -
1071 GLU   ( 106-)  C  -
And so on for a total of 180 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     9.26    33.73
  95 HIS   (  98-)  A  -   CA     8.4    49.47    34.11
  95 HIS   (  98-)  A  -   C      8.5    12.93     0.15
 134 PRO   ( 137-)  A  -   N      6.1    17.56    -2.48
 261 ASP   ( 264-)  A  -   CA     7.8    49.31    33.73
 337 LEU   ( 341-)  A  -   CA    -8.5    21.16    34.19
 443 GLN   ( 447-)  A  -   CA   -12.3    10.23    33.96
 476 ILE   ( 480-)  A  -   CB     6.6    40.85    32.31
 615 THR   ( 625-)  A  -   CB     6.5    48.69    34.09
 618 GLY   ( 628-)  A  -   C     -6.2    -8.17     0.06
 626 LYS   ( 637-)  A  -   C    -17.5   -26.31     0.11
 635 THR   ( 648-)  A  -   CB   -13.7     3.48    34.09
 636 VAL   ( 649-)  A  -   C      7.9    10.93     0.15
 636 VAL   ( 649-)  A  -   CB   -35.1   -78.93   -32.96
 685 ASN   ( 698-)  A  -   C     -6.0    -9.21     0.27
 741 THR   ( 756-)  A  -   CA     6.5    44.75    33.84
 746 HIS   ( 762-)  A  -   CA    -7.2    20.85    34.11
 815 MET   ( 832-)  A  -   CA    -7.5    20.64    34.17
 822 PRO   ( 840-)  A  -   N     -6.2   -22.83    -2.48
 828 GLU   (  21-)  B  -   C      6.5     9.44    -0.03
 829 THR   (  22-)  B  -   C      7.5    11.51     0.30
 831 ILE   (  24-)  B  -   C      6.4     8.36     0.03
 852 ASP   (  45-)  B  -   C      6.3     9.70    -0.01
 859 ALA   (  52-)  B  -   C      6.2     9.53     0.08
 868 ASN   (  61-)  B  -   C      6.6    10.69     0.27
And so on for a total of 312 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.

7011 ARG   ( 335-)  1  -   7.43
1069  ARG  ( 335-) W  -   7.43
7749 ARG   ( 335-)  3  -   7.43
8864 ARG   ( 335-)  6  -   7.41
1142  ARG  ( 335-) Y  -   7.41
8493 ARG   ( 335-)  5  -   7.40
1179  ARG  ( 335-) Z  -   7.40
7381 ARG   ( 335-)  2  -   7.38
8121 ARG   ( 335-)  4  -   7.38
9235 ARG   ( 335-)  7  -   7.37
1105  ARG  ( 335-) X  -   7.35
4106 ALA   ( 784-)  J  -   6.69
6335 ALA   ( 784-)  P  -   6.67
5220 ALA   ( 784-)  M  -   6.66
1880 ALA   ( 784-)  D  -   6.64
 768 ALA   ( 784-)  A  -   6.52
2993 ALA   ( 784-)  G  -   6.49
4669 GLU   ( 219-)  M  -   6.30
2438 GLU   ( 219-)  G  -   6.30
3557 GLU   ( 219-)  J  -   6.29
5782 GLU   ( 219-)  P  -   6.28
 216 GLU   ( 219-)  A  -   6.27
1330 GLU   ( 219-)  D  -   6.21
7779 ALA   ( 365-)  3  -   6.14
1071  ALA  ( 365-) W  -   6.14
And so on for a total of 296 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 : 1.672

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.

3182 TYR   ( 150-)  H  -  15.56
6524 TYR   ( 150-)  Q  -  15.55
2067 TYR   ( 150-)  E  -  15.55
4294 TYR   ( 150-)  K  -  15.49
 955 TYR   ( 150-)  B  -  15.42
5408 TYR   ( 150-)  N  -  15.41
4322 ASP   (  18-)  L  -   9.79
6552 ASP   (  18-)  R  -   9.77
3210 ASP   (  18-)  I  -   9.75
2095 ASP   (  18-)  F  -   9.72
5436 ASP   (  18-)  O  -   9.67
 983 ASP   (  18-)  C  -   9.66
2027 ASP   ( 107-)  E  -   8.30
 914 ASP   ( 107-)  B  -   8.27
6483 ASP   ( 107-)  Q  -   8.21
3141 ASP   ( 107-)  H  -   8.18
4253 ASP   ( 107-)  K  -   8.17
5367 ASP   ( 107-)  N  -   8.12
4393 GLU   (  89-)  L  -   7.00
6622 GLU   (  89-)  R  -   6.95
5507 GLU   (  89-)  O  -   6.95
3281 GLU   (  89-)  I  -   6.87
1054 GLU   (  89-)  C  -   6.83
2165 GLU   (  89-)  F  -   6.77
5419 GLU   ( 161-)  N  -   5.85
And so on for a total of 109 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.

 613 PHE   ( 623-)  A  -   CB   7.04
6180 PHE   ( 623-)  P  -   CB   7.02
3958 PHE   ( 623-)  J  -   CB   7.01
1729 PHE   ( 623-)  D  -   CB   6.99
5066 PHE   ( 623-)  M  -   CB   6.99
2842 PHE   ( 623-)  G  -   CB   6.97
1145  HIS  ( 371-) Y  -    CB   5.62
1182  HIS  ( 371-) Z  -    CB   5.60
9271 HIS   ( 371-)  7  -   CB   5.60
8900 HIS   ( 371-)  6  -   CB   5.59
7046 HIS   ( 371-)  1  -   CB   5.59
1036  HIS  ( 371-) V  -    CB   5.59
7785 HIS   ( 371-)  3  -   CB   5.59
8157 HIS   ( 371-)  4  -   CB   5.58
1072  HIS  ( 371-) W  -    CB   5.58
9633 HIS   ( 371-)  8  -   CB   5.58
1000  HIS  ( 371-) 9  -    CB   5.58
1109  HIS  ( 371-) X  -    CB   5.58
8529 HIS   ( 371-)  5  -   CB   5.57
7417 HIS   ( 371-)  2  -   CB   5.57
9804 HIS   ( 173-)  9  -   CB   4.19
6851 HIS   ( 173-)  1  -   CB   4.19
7959 HIS   ( 173-)  4  -   CB   4.18
8703 HIS   ( 173-)  6  -   CB   4.18
1163  HIS  ( 173-) Z  -    CB   4.18
1053  HIS  ( 173-) W  -    CB   4.17
9441 HIS   ( 173-)  8  -   CB   4.17
7219 HIS   ( 173-)  2  -   CB   4.17
1089  HIS  ( 173-) X  -    CB   4.17
7589 HIS   ( 173-)  3  -   CB   4.17
1126  HIS  ( 173-) Y  -    CB   4.17
8331 HIS   ( 173-)  5  -   CB   4.17
1017  HIS  ( 173-) V  -    CB   4.16
9074 HIS   ( 173-)  7  -   CB   4.16
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.491

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 : -4.491

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
6516 PRO   ( 141-)  Q  -   -2.9
3175 PRO   ( 141-)  H  -   -2.9
 948 PRO   ( 141-)  B  -   -2.9
4286 PRO   ( 141-)  K  -   -2.9
5400 PRO   ( 141-)  N  -   -2.9
6381 PRO   ( 830-)  P  -   -2.9
3039 PRO   ( 830-)  G  -   -2.9
 813 PRO   ( 830-)  A  -   -2.9
1926 PRO   ( 830-)  D  -   -2.9
5265 PRO   ( 830-)  M  -   -2.9
4151 PRO   ( 830-)  J  -   -2.9
 126 TYR   ( 129-)  A  -   -2.8
2350 TYR   ( 129-)  G  -   -2.8
1240 TYR   ( 129-)  D  -   -2.8
4579 TYR   ( 129-)  M  -   -2.8
5693 TYR   ( 129-)  P  -   -2.8
3467 TYR   ( 129-)  J  -   -2.8
6338 ILE   ( 787-)  P  -   -2.8
8267 PRO   ( 109-)  5  -   -2.8
8639 PRO   ( 109-)  6  -   -2.8
7525 PRO   ( 109-)  3  -   -2.8
7895 PRO   ( 109-)  4  -   -2.8
1083  PRO  ( 109-) X  -   -2.8
1156  PRO  ( 109-) Z  -   -2.8
And so on for a total of 656 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
 636 VAL   ( 649-)  A  - omega poor
 637 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 : -4.604

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
1447 SER   ( 336-)  D  -   0.33
2555 SER   ( 336-)  G  -   0.33
3674 SER   ( 336-)  J  -   0.33
4786 SER   ( 336-)  M  -   0.33
5899 SER   ( 336-)  P  -   0.33
 156 SER   ( 159-)  A  -   0.36
1270 SER   ( 159-)  D  -   0.36
2379 SER   ( 159-)  G  -   0.36
3497 SER   ( 159-)  J  -   0.36
4609 SER   ( 159-)  M  -   0.36
5723 SER   ( 159-)  P  -   0.36
 416 SER   ( 420-)  A  -   0.37
1529 SER   ( 420-)  D  -   0.37
2639 SER   ( 420-)  G  -   0.37
3755 SER   ( 420-)  J  -   0.37
4866 SER   ( 420-)  M  -   0.37
5980 SER   ( 420-)  P  -   0.37
6957 SER   ( 281-)  1  -   0.39
9911 SER   ( 281-)  9  -   0.39
1064  SER  ( 281-) W  -   0.39
1136  SER  ( 281-) Y  -   0.39
7327 SER   ( 281-)  2  -   0.40
7697 SER   ( 281-)  3  -   0.40
8067 SER   ( 281-)  4  -   0.40
8439 SER   ( 281-)  5  -   0.40
8810 SER   ( 281-)  6  -   0.40
9182 SER   ( 281-)  7  -   0.40
9549 SER   ( 281-)  8  -   0.40
1027  SER  ( 281-) V  -   0.40
1100  SER  ( 281-) X  -   0.40
1173  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 4641 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!

5631 GLY   (  67-)  P  -  2.50   80
2288 GLY   (  67-)  G  -  2.50   80
  64 GLY   (  67-)  A  -  2.50   80
3405 GLY   (  67-)  J  -  2.50   80
4517 GLY   (  67-)  M  -  2.50   80
1178 GLY   (  67-)  D  -  2.50   80
2748 PRO   ( 529-)  G  -  2.40   10
1638 PRO   ( 529-)  D  -  2.40   10
 523 PRO   ( 529-)  A  -  2.29   11
4975 PRO   ( 529-)  M  -  2.29   11
6089 PRO   ( 529-)  P  -  2.29   11
3864 PRO   ( 529-)  J  -  2.29   11
3618 PRO   ( 280-)  J  -  2.20   10
5843 PRO   ( 280-)  P  -  2.20   10
4730 PRO   ( 280-)  M  -  2.20   10
1391 PRO   ( 280-)  D  -  2.20   10
2499 PRO   ( 280-)  G  -  2.20   10
 277 PRO   ( 280-)  A  -  2.20   10
1517 GLY   ( 407-)  D  -  2.03   16
2626 GLY   ( 407-)  G  -  2.03   16
 403 GLY   ( 407-)  A  -  2.03   16
6190 GLY   ( 635-)  P  -  1.94   10
1123  GLY  ( 146-) Y  -  1.59   80
7192 GLY   ( 146-)  2  -  1.59   80
1087  GLY  ( 146-) X  -  1.59   80
8304 GLY   ( 146-)  5  -  1.59   80
7932 GLY   ( 146-)  4  -  1.58   80
8676 GLY   ( 146-)  6  -  1.58   80
7562 GLY   ( 146-)  3  -  1.58   80
9047 GLY   ( 146-)  7  -  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  -   0.13 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  -   0.12 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
 656 PRO   ( 669-)  A  -   0.13 LOW
 664 PRO   ( 677-)  A  -   0.02 LOW
 670 PRO   ( 683-)  A  -   0.10 LOW
And so on for a total of 285 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  -  171.6 envelop N (180 degrees)
 813 PRO   ( 830-)  A  -  156.2 half-chair C-alpha/N (162 degrees)
 948 PRO   ( 141-)  B  - -160.1 half-chair N/C-delta (-162 degrees)
1006 PRO   (  41-)  C  -  -10.1 half-chair C-alpha/N (-18 degrees)
1264 PRO   ( 153-)  D  -  171.5 envelop N (180 degrees)
1926 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  -  -10.5 half-chair C-alpha/N (-18 degrees)
2373 PRO   ( 153-)  G  -  171.7 envelop N (180 degrees)
3039 PRO   ( 830-)  G  -  156.7 half-chair C-alpha/N (162 degrees)
3175 PRO   ( 141-)  H  - -159.6 half-chair N/C-delta (-162 degrees)
3233 PRO   (  41-)  I  -  -10.8 half-chair C-alpha/N (-18 degrees)
3491 PRO   ( 153-)  J  -  171.5 envelop N (180 degrees)
4151 PRO   ( 830-)  J  -  156.7 half-chair C-alpha/N (162 degrees)
4286 PRO   ( 141-)  K  - -160.3 half-chair N/C-delta (-162 degrees)
4345 PRO   (  41-)  L  -  -10.6 half-chair C-alpha/N (-18 degrees)
4603 PRO   ( 153-)  M  -  171.5 envelop N (180 degrees)
5265 PRO   ( 830-)  M  -  156.4 half-chair C-alpha/N (162 degrees)
5400 PRO   ( 141-)  N  - -160.6 half-chair N/C-delta (-162 degrees)
5459 PRO   (  41-)  O  -  -10.5 half-chair C-alpha/N (-18 degrees)
5717 PRO   ( 153-)  P  -  171.5 envelop N (180 degrees)
6381 PRO   ( 830-)  P  -  157.0 half-chair C-alpha/N (162 degrees)
6516 PRO   ( 141-)  Q  - -160.3 half-chair N/C-delta (-162 degrees)
6575 PRO   (  41-)  R  -  -10.6 half-chair C-alpha/N (-18 degrees)
6789 PRO   ( 109-)  1  -  112.4 envelop C-beta (108 degrees)
7155 PRO   ( 109-)  2  -  112.4 envelop C-beta (108 degrees)
7525 PRO   ( 109-)  3  -  112.3 envelop C-beta (108 degrees)
7895 PRO   ( 109-)  4  -  112.3 envelop C-beta (108 degrees)
8267 PRO   ( 109-)  5  -  112.3 envelop C-beta (108 degrees)
8639 PRO   ( 109-)  6  -  112.2 envelop C-beta (108 degrees)
9010 PRO   ( 109-)  7  -  112.3 envelop C-beta (108 degrees)
9379 PRO   ( 109-)  8  -  112.3 envelop C-beta (108 degrees)
9741 PRO   ( 109-)  9  -  112.4 envelop C-beta (108 degrees)
1010  PRO  ( 109-) V  -  112.3 envelop C-beta (108 degrees)
1047  PRO  ( 109-) W  -  112.3 envelop C-beta (108 degrees)
1083  PRO  ( 109-) X  -  112.4 envelop C-beta (108 degrees)
1119  PRO  ( 109-) Y  -  112.4 envelop C-beta (108 degrees)
1156  PRO  ( 109-) Z  -  112.3 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
 928 LEU   ( 121-)  B  -   CD1  <->   935 PHE   ( 128-)  B  -   CD2  2.62    0.58  INTRA
3155 LEU   ( 121-)  H  -   CD1  <->  3162 PHE   ( 128-)  H  -   CD2  2.62    0.58  INTRA
6496 LEU   ( 121-)  Q  -   CD1  <->  6503 PHE   ( 128-)  Q  -   CD2  2.62    0.58  INTRA
4267 LEU   ( 121-)  K  -   CD1  <->  4274 PHE   ( 128-)  K  -   CD2  2.61    0.59  INTRA
5380 LEU   ( 121-)  N  -   CD1  <->  5387 PHE   ( 128-)  N  -   CD2  2.61    0.59  INTRA
2856 LYS   ( 642-)  G  -   CE   <->  1033  SER  ( 344-) V  -    CB   2.45    0.75  INTRA
6197 LYS   ( 642-)  P  -   CE   <->  7020 SER   ( 344-)  1  -   CB   2.45    0.75  INTRA
5081 LYS   ( 642-)  M  -   CE   <->  1180  SER  ( 344-) Z  -    CB   2.45    0.75  INTRA
1743 LYS   ( 642-)  D  -   CE   <->  9973 SER   ( 344-)  9  -   CB   2.45    0.75  INTRA
6880 THR   ( 202-)  1  -   N    <->  1137  ILE  ( 287-) Y  -    CD1  2.35    0.75  INTRA
2724 MLY   ( 505-)  G  -   CH2  <->  2972 HIS   ( 762-)  G  -   CE1  2.33    0.87  INTRA
6512 TRP   ( 137-)  Q  -   CH2  <->  6520 GLY   ( 146-)  Q  -   N    2.29    0.81  INTRA
5396 TRP   ( 137-)  N  -   CH2  <->  5404 GLY   ( 146-)  N  -   N    2.29    0.81  INTRA
 944 TRP   ( 137-)  B  -   CH2  <->   952 GLY   ( 146-)  B  -   N    2.29    0.81  INTRA
2055 TRP   ( 137-)  E  -   CH2  <->  2063 GLY   ( 146-)  E  -   N    2.29    0.81  INTRA
3171 TRP   ( 137-)  H  -   CH2  <->  3179 GLY   ( 146-)  H  -   N    2.29    0.81  INTRA
4992 THR   ( 548-)  M  -   CG2  <->  7094 GLY   (  48-)  2  -   N    2.22    0.88  INTRA
5077 LYS   ( 637-)  M  -   C    <->  1180  ILE  ( 345-) Z  -    CD1  2.21    0.99  INTRA
2314 MET   (  93-)  G  -   CG   <->  2926 ARG   ( 714-)  G  -   O    2.21    0.59  INTRA
1737 GLY   ( 632-)  D  -   C    <->  9657 ASP   (  25-)  9  -   N    2.19    0.91  INTRA
6113 ASP   ( 556-)  P  -   OD2  <->  7459 GLN   (  41-)  3  -   NE2  2.18    0.52  INTRA
1824 TYR   ( 724-)  D  -   O    <->  1878 MLY   ( 782-)  D  -   CH2  2.15    0.65  INTRA
 797 PHE   ( 814-)  A  -   CD1  <->   934 ARG   ( 127-)  B  -   NH2  2.14    0.96  INTRA
3553 GLN   ( 215-)  J  -   CD   <->  3677 ILE   ( 340-)  J  -   N    2.12    0.98  INTRA
And so on for a total of 8186 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.

 984 ARG   (  19-)  C  -     -7.75
4323 ARG   (  19-)  L  -     -7.73
3211 ARG   (  19-)  I  -     -7.70
5437 ARG   (  19-)  O  -     -7.70
6553 ARG   (  19-)  R  -     -7.69
2096 ARG   (  19-)  F  -     -7.52
1004  GLN  (  41-) V  -     -7.52
1150  GLN  (  41-) Z  -     -7.52
1076  GLN  (  41-) X  -     -7.52
6721 GLN   (  41-)  1  -     -7.52
9673 GLN   (  41-)  9  -     -7.52
8571 GLN   (  41-)  6  -     -7.51
1040  GLN  (  41-) W  -     -7.51
8942 GLN   (  41-)  7  -     -7.51
1113  GLN  (  41-) Y  -     -7.51
8199 GLN   (  41-)  5  -     -7.51
7827 GLN   (  41-)  4  -     -7.51
9311 GLN   (  41-)  8  -     -7.50
3467 TYR   ( 129-)  J  -     -7.41
5693 TYR   ( 129-)  P  -     -7.41
4579 TYR   ( 129-)  M  -     -7.41
1240 TYR   ( 129-)  D  -     -7.41
 126 TYR   ( 129-)  A  -     -7.41
2350 TYR   ( 129-)  G  -     -7.40
7459 GLN   (  41-)  3  -     -7.30
And so on for a total of 335 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
1259 ARG   ( 148-)  D  -   1261 - GLU    150- ( D)  -      -4.73
1682 GLU   ( 576-)  D  -   1684 - HIS    578- ( D)  -      -4.29
2795 GLU   ( 576-)  G  -   2797 - HIS    578- ( G)  -      -4.26
2920 ARG   ( 708-)  G  -   2922 - GLY    710- ( G)  -      -4.57
3486 ARG   ( 148-)  J  -   3488 - GLU    150- ( J)  -      -4.69
3911 GLU   ( 576-)  J  -   3913 - HIS    578- ( J)  -      -4.26
4598 ARG   ( 148-)  M  -   4600 - GLU    150- ( M)  -      -4.78
5019 GLU   ( 576-)  M  -   5021 - HIS    578- ( M)  -      -4.27
5146 ARG   ( 708-)  M  -   5148 - GLY    710- ( M)  -      -4.55
6133 GLU   ( 576-)  P  -   6135 - HIS    578- ( P)  -      -4.28
6719 ARG   (  39-)  1  -   6721 - GLN     41- ( 1)  -      -6.73
7086 ARG   (  39-)  2  -   7088 - GLN     41- ( 2)  -      -6.63
7457 ARG   (  39-)  3  -   7459 - GLN     41- ( 3)  -      -6.67
7825 ARG   (  39-)  4  -   7827 - GLN     41- ( 4)  -      -6.74
8197 ARG   (  39-)  5  -   8199 - GLN     41- ( 5)  -      -6.74
8569 ARG   (  39-)  6  -   8571 - GLN     41- ( 6)  -      -6.73
8940 ARG   (  39-)  7  -   8942 - GLN     41- ( 7)  -      -6.73
9309 ARG   (  39-)  8  -   9311 - GLN     41- ( 8)  -      -6.71
9671 ARG   (  39-)  9  -   9673 - GLN     41- ( 9)  -      -6.72
1003  ARG  (  39-) V  -    1004 -  GLN    41- (V ) -       -6.72
1040  ARG  (  39-) W  -    1040 -  GLN    41- (W ) -       -6.72
1076  ARG  (  39-) X  -    1076 -  GLN    41- (X ) -       -6.75
1113  ARG  (  39-) Y  -    1113 -  GLN    41- (Y ) -       -6.73
1149  ARG  (  39-) Z  -    1150 -  GLN    41- (Z ) -       -6.71

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.

 971 ALA   (   6-)  C  -  -3.14
2083 ALA   (   6-)  F  -  -3.14
3198 ALA   (   6-)  I  -  -3.14
 109 ALA   ( 112-)  A  -  -2.88
4562 ALA   ( 112-)  M  -  -2.88
2333 ALA   ( 112-)  G  -  -2.88
5676 ALA   ( 112-)  P  -  -2.88
1223 ALA   ( 112-)  D  -  -2.88
3450 ALA   ( 112-)  J  -  -2.88
8570 HIS   (  40-)  6  -  -2.88
6789 PRO   ( 109-)  1  -  -2.85
1047  PRO  ( 109-) W  -  -2.85
1119  PRO  ( 109-) Y  -  -2.85
1010  PRO  ( 109-) V  -  -2.85
1083  PRO  ( 109-) X  -  -2.85
7155 PRO   ( 109-)  2  -  -2.85
1156  PRO  ( 109-) Z  -  -2.85
5408 TYR   ( 150-)  N  -  -2.69
2067 TYR   ( 150-)  E  -  -2.68
6524 TYR   ( 150-)  Q  -  -2.68
9334 ILE   (  64-)  8  -  -2.66
1006  ILE  (  64-) V  -  -2.65
6264 GLY   ( 710-)  P  -  -2.63
 460 ILE   ( 464-)  A  -  -2.62
4838 LEU   ( 389-)  M  -  -2.62
 385 LEU   ( 389-)  A  -  -2.62
2608 LEU   ( 389-)  G  -  -2.62
5952 LEU   ( 389-)  P  -  -2.62
3726 LEU   ( 389-)  J  -  -2.62
1499 LEU   ( 389-)  D  -  -2.62
2683 ILE   ( 464-)  G  -  -2.61
4910 ILE   ( 464-)  M  -  -2.61
1573 ILE   ( 464-)  D  -  -2.61
3799 ILE   ( 464-)  J  -  -2.61
6024 ILE   ( 464-)  P  -  -2.61
 934 ARG   ( 127-)  B  -  -2.59
9696 ILE   (  64-)  9  -  -2.55
3912 ALA   ( 577-)  J  -  -2.55
8965 ILE   (  64-)  7  -  -2.54
8394 LEU   ( 236-)  5  -  -2.53
7720 MET   ( 305-)  3  -  -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.

 585 TRP   ( 595-)  A  -  -  588 MLY   ( 598-)  A  -   -251.21
1701 TRP   ( 595-)  D  -  - 1704 MLY   ( 598-)  D  -   -251.21
1740 GLY   ( 639-)  D  -  - 1744 GLY   ( 643-)  D  -     -1.69
1936 PRO   ( 840-)  D  -  - 1939 LYS   ( 843-)  D  -     -1.97
2814 TRP   ( 595-)  G  -  - 2817 MLY   ( 598-)  G  -   -251.21
3049 PRO   ( 840-)  G  -  - 3052 LYS   ( 843-)  G  -     -2.03
3930 TRP   ( 595-)  J  -  - 3933 MLY   ( 598-)  J  -   -251.21
4161 PRO   ( 840-)  J  -  - 4164 LYS   ( 843-)  J  -     -1.82
5038 TRP   ( 595-)  M  -  - 5041 MLY   ( 598-)  M  -   -251.21
5078 GLY   ( 639-)  M  -  - 5082 GLY   ( 643-)  M  -     -1.69
5275 PRO   ( 840-)  M  -  - 5278 LYS   ( 843-)  M  -     -1.94
6152 TRP   ( 595-)  P  -  - 6155 MLY   ( 598-)  P  -   -251.22
6195 LYS   ( 640-)  P  -  - 6198 GLY   ( 643-)  P  -     -2.02
6391 PRO   ( 840-)  P  -  - 6394 LYS   ( 843-)  P  -     -1.95
1182  ILE  ( 369-) Z  -   - 1182  ARG  ( 372-) Z  -      -1.73
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  -
 645 ASN   ( 658-)  A  -
 675 HIS   ( 688-)  A  -
1238 ASN   ( 127-)  D  -
1590 ASN   ( 481-)  D  -
1697 ASN   ( 591-)  D  -
1758 ASN   ( 658-)  D  -
2348 ASN   ( 127-)  G  -
2700 ASN   ( 481-)  G  -
2810 ASN   ( 591-)  G  -
2870 ASN   ( 658-)  G  -
2972 HIS   ( 762-)  G  -
3465 ASN   ( 127-)  J  -
3816 ASN   ( 481-)  J  -
3926 ASN   ( 591-)  J  -
3986 ASN   ( 658-)  J  -
4016 HIS   ( 688-)  J  -
4138 GLN   ( 817-)  J  -
4577 ASN   ( 127-)  M  -
4927 ASN   ( 481-)  M  -
5034 ASN   ( 591-)  M  -
5096 ASN   ( 658-)  M  -
And so on for a total of 63 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
 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
 146 GLN   ( 149-)  A  -   N
And so on for a total of 1681 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.

  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
 472 GLU   ( 476-)  A  -   OE2
 495 GLU   ( 499-)  A  -   OE1
 568 HIS   ( 578-)  A  -   ND1
 579 ASP   ( 589-)  A  -   OD2
 589 ASN   ( 599-)  A  -   OD1
 619 GLU   ( 629-)  A  -   OE1
 642 GLU   ( 655-)  A  -   OE2
 685 ASN   ( 698-)  A  -   OD1
 706 ASP   ( 719-)  A  -   OD1
 842 ASP   (  35-)  B  -   OD1
 843 GLN   (  36-)  B  -   OE1
 966 GLU   ( 161-)  B  -   OE1
1005 ASN   (  40-)  C  -   OD1
1022 GLU   (  57-)  C  -   OE2
1060 ASP   (  95-)  C  -   OD2
1197 ASP   (  86-)  D  -   OD2
1207 HIS   (  96-)  D  -   ND1
And so on for a total of 310 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
 706 ASP   ( 719-)  A  -  H-bonding suggests Asn
 737 ASP   ( 752-)  A  -  H-bonding suggests Asn
 791 GLU   ( 808-)  A  -  H-bonding suggests Gln
 832 GLU   (  25-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
 833 ASP   (  26-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 836 GLU   (  29-)  B  -  H-bonding suggests Gln
 842 ASP   (  35-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 856 GLU   (  49-)  B  -  H-bonding suggests Gln
 872 ASP   (  65-)  B  -  H-bonding suggests Asn
 893 GLU   (  86-)  B  -  H-bonding suggests Gln
 899 ASP   (  92-)  B  -  H-bonding suggests Asn
 912 ASP   ( 105-)  B  -  H-bonding suggests Asn
 926 GLU   ( 119-)  B  -  H-bonding suggests Gln
 954 ASP   ( 149-)  B  -  H-bonding suggests Asn
 977 GLU   (  12-)  C  -  H-bonding suggests Gln; but Alt-Rotamer
 983 ASP   (  18-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
1054 GLU   (  89-)  C  -  H-bonding suggests Gln
1060 ASP   (  95-)  C  -  H-bonding suggests Asn
And so on for a total of 234 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 :  -1.879
  2nd generation packing quality :  -1.950
  Ramachandran plot appearance   :  -4.491 (bad)
  chi-1/chi-2 rotamer normality  :  -4.604 (bad)
  Backbone conformation          :  -1.046

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.959
  Bond angles                    :   1.538
  Omega angle restraints         :   0.748
  Side chain planarity           :   1.481
  Improper dihedral distribution :   1.853 (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                   :   0.959
  Bond angles                    :   1.538
  Omega angle restraints         :   0.748
  Side chain planarity           :   1.481
  Improper dihedral distribution :   1.853 (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.