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 pdb1o19.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 : 7.320
CA-only RMS fit for the two chains : 7.312

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 : 12.455

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 : 17.214
CA-only RMS fit for the two chains : 17.263

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 : 4.618
CA-only RMS fit for the two chains : 4.602

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 S

All-atom RMS fit for the two chains : 14.731
CA-only RMS fit for the two chains : 14.772

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 S

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  -
 816 ASN   ( 819-)  A  -
 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 164 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: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

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: S

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: T

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: U

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  -
2098 ARG   (  19-)  F  -
2114 ARG   (  35-)  F  -
2170 ARG   (  92-)  F  -
2186 ARG   ( 108-)  F  -
3214 ARG   (  19-)  I  -
3230 ARG   (  35-)  I  -
3287 ARG   (  92-)  I  -
3303 ARG   ( 108-)  I  -
4327 ARG   (  19-)  L  -
4343 ARG   (  35-)  L  -
4400 ARG   (  92-)  L  -
4416 ARG   ( 108-)  L  -
5440 ARG   (  19-)  O  -
5456 ARG   (  35-)  O  -
5513 ARG   (  92-)  O  -
5529 ARG   ( 108-)  O  -
6556 ARG   (  19-)  U  -
6572 ARG   (  35-)  U  -
6629 ARG   (  92-)  U  -
6645 ARG   ( 108-)  U  -

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  -
2069 TYR   ( 150-)  E  -
2217 TYR   ( 139-)  F  -
3185 TYR   ( 150-)  H  -
3334 TYR   ( 139-)  I  -
4298 TYR   ( 150-)  K  -
4447 TYR   ( 139-)  L  -
5411 TYR   ( 150-)  N  -
5560 TYR   ( 139-)  O  -
6527 TYR   ( 150-)  T  -
6676 TYR   ( 139-)  U  -

Warning: Phenylalanine convention problem

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

 839 PHE   (  31-)  B  -
 888 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  -
1953 PHE   (  31-)  E  -
2002 PHE   (  80-)  E  -
2022 PHE   ( 101-)  E  -
2036 PHE   ( 116-)  E  -
2060 PHE   ( 140-)  E  -
2093 PHE   (  14-)  F  -
2096 PHE   (  17-)  F  -
2143 PHE   (  65-)  F  -
2165 PHE   (  87-)  F  -
2172 PHE   (  94-)  F  -
3068 PHE   (  31-)  H  -
3117 PHE   (  80-)  H  -
3138 PHE   ( 101-)  H  -
3153 PHE   ( 116-)  H  -
3177 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.

 828 ASP   (  20-)  B  -
 834 ASP   (  26-)  B  -
 853 ASP   (  45-)  B  -
 854 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  -
1942 ASP   (  20-)  E  -
1948 ASP   (  26-)  E  -
1967 ASP   (  45-)  E  -
1968 ASP   (  46-)  E  -
2016 ASP   (  95-)  E  -
2068 ASP   ( 149-)  E  -
2081 ASP   ( 162-)  E  -
2087 ASP   (   8-)  F  -
2111 ASP   (  32-)  F  -
2164 ASP   (  86-)  F  -
2173 ASP   (  95-)  F  -
3057 ASP   (  20-)  H  -
3063 ASP   (  26-)  H  -
3082 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.

 831 GLU   (  23-)  B  -
 833 GLU   (  25-)  B  -
 837 GLU   (  29-)  B  -
 857 GLU   (  49-)  B  -
 878 GLU   (  70-)  B  -
 894 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  -
1945 GLU   (  23-)  E  -
1947 GLU   (  25-)  E  -
1951 GLU   (  29-)  E  -
1971 GLU   (  49-)  E  -
1992 GLU   (  70-)  E  -
2008 GLU   (  86-)  E  -
2091 GLU   (  12-)  F  -
2145 GLU   (  67-)  F  -
2163 GLU   (  85-)  F  -
2167 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    4.4
  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    4.6
  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    5.1
 199 SER   ( 202-)  A  -   N   -C     1.25   -4.2
 214 THR   ( 217-)  A  -   CA   CB    1.61    4.1
 215 LEU   ( 218-)  A  -   CB   CG    1.68    7.7
 216 GLU   ( 219-)  A  -   N   -C     1.21   -5.8
 238 ASP   ( 241-)  A  -   CG   OD1   1.34    4.7
 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    4.3
 327 GLU   ( 330-)  A  -   CD   OE1   1.33    4.1
 342 ASP   ( 346-)  A  -   CG   OD2   1.33    4.4
 343 GLU   ( 347-)  A  -   CD   OE1   1.33    4.5
 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    4.9
 430 TYR   ( 434-)  A  -   CA   CB    1.44   -4.5
 472 GLU   ( 476-)  A  -   CD   OE1   1.35    5.2
And so on for a total of 422 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

 |  1.002013  0.000088  0.000000|
 |  0.000088  1.001942 -0.000056|
 |  0.000000 -0.000056  1.001622|
Proposed new scale matrix

 |  0.003326  0.000000  0.000000|
 |  0.000000  0.003327  0.000000|
 |  0.000000  0.000000  0.003328|
With corresponding cell

    A    = 300.634  B   = 300.613  C    = 300.517
    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: 1302.246
(Under-)estimated Z-score: 26.596

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  118.63    4.5
  35 VAL   (  38-)  A  -   N    CA   CB  102.72   -4.6
  44 PHE   (  47-)  A  -   C    CA   CB  100.96   -4.8
  68 THR   (  71-)  A  -   N    CA   CB  117.34    4.0
  72 ASP   (  75-)  A  -   N    CA   CB  122.96    7.3
  72 ASP   (  75-)  A  -   C    CA   CB  117.75    4.0
  79 PRO   (  82-)  A  -   N    CA   CB  109.35    5.8
  85 ILE   (  88-)  A  -   CB   CG1  CD1 101.51   -5.9
  95 HIS   (  98-)  A  -   C    CA   CB   87.32  -12.0
  95 HIS   (  98-)  A  -   CD2  CG   ND1 110.35    4.3
 101 TYR   ( 104-)  A  -   C    CA   CB  117.79    4.0
 115 TYR   ( 118-)  A  -   C    CA   CB  101.39   -4.6
 125 PRO   ( 128-)  A  -   N    CA   CB  108.13    4.7
 134 PRO   ( 137-)  A  -  -CA  -C    N   108.45   -5.6
 138 LEU   ( 141-)  A  -   C    CA   CB   97.98   -6.4
 150 PRO   ( 153-)  A  -   N    CA   CB  107.43    4.0
 158 ASN   ( 161-)  A  -   CA   CB   CG  107.59   -5.0
 158 ASN   ( 161-)  A  -   ND2  CG   OD1 127.43    4.8
 162 PHE   ( 165-)  A  -   N    CA   CB  100.29   -6.0
 162 PHE   ( 165-)  A  -   CA   CB   CG  108.79   -5.0
 169 ASN   ( 172-)  A  -   N    CA   CB  118.19    4.5
 170 GLN   ( 173-)  A  -   N    CA   CB  102.94   -4.4
 177 GLU   ( 180-)  A  -   N    CA   CB  118.51    4.7
 189 VAL   ( 192-)  A  -   CA   CB   CG1 102.03   -5.0
 193 PHE   ( 196-)  A  -   CA   CB   CG  108.17   -5.6
And so on for a total of 3091 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.

 828 ASP   (  20-)  B  -
 831 GLU   (  23-)  B  -
 833 GLU   (  25-)  B  -
 834 ASP   (  26-)  B  -
 837 GLU   (  29-)  B  -
 853 ASP   (  45-)  B  -
 854 ASP   (  46-)  B  -
 857 GLU   (  49-)  B  -
 878 GLU   (  70-)  B  -
 894 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     9.23    33.73
  95 HIS   (  98-)  A  -   CA     8.4    49.48    34.11
  95 HIS   (  98-)  A  -   C      8.6    12.99     0.15
 134 PRO   ( 137-)  A  -   N      6.1    17.58    -2.48
 261 ASP   ( 264-)  A  -   CA     7.8    49.24    33.73
 337 LEU   ( 341-)  A  -   CA    -8.6    21.11    34.19
 443 GLN   ( 447-)  A  -   CA   -12.3    10.31    33.96
 476 ILE   ( 480-)  A  -   CB     6.6    40.85    32.31
 615 THR   ( 625-)  A  -   CB     6.5    48.68    34.09
 618 GLY   ( 628-)  A  -   C     -6.2    -8.15     0.06
 626 LYS   ( 637-)  A  -   C    -17.5   -26.29     0.11
 635 THR   ( 648-)  A  -   CB   -13.7     3.48    34.09
 636 VAL   ( 649-)  A  -   C      7.9    10.99     0.15
 636 VAL   ( 649-)  A  -   CB   -35.1   -78.94   -32.96
 685 ASN   ( 698-)  A  -   C     -6.1    -9.26     0.27
 741 THR   ( 756-)  A  -   CA     6.6    44.79    33.84
 746 HIS   ( 762-)  A  -   CA    -7.2    20.91    34.11
 815 MET   ( 832-)  A  -   CA    -7.5    20.61    34.17
 823 PRO   ( 840-)  A  -   N     -6.2   -22.87    -2.48
 829 GLU   (  21-)  B  -   C      6.6     9.51    -0.03
 830 THR   (  22-)  B  -   C      7.5    11.50     0.30
 832 ILE   (  24-)  B  -   C      6.4     8.36     0.03
 853 ASP   (  45-)  B  -   C      6.3     9.72    -0.01
 860 ALA   (  52-)  B  -   C      6.2     9.56     0.08
 869 ASN   (  61-)  B  -   C      6.7    10.73     0.27
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.

7387 ARG   ( 335-)  2  -   7.45
8127 ARG   ( 335-)  4  -   7.44
1069  ARG  ( 335-) W  -   7.41
1106  ARG  ( 335-) X  -   7.41
1143  ARG  ( 335-) Y  -   7.39
8499 ARG   ( 335-)  5  -   7.39
7757 ARG   ( 335-)  3  -   7.39
8871 ARG   ( 335-)  6  -   7.38
9242 ARG   ( 335-)  7  -   7.38
1179  ARG  ( 335-) Z  -   7.37
7019 ARG   ( 335-)  1  -   7.35
4110 ALA   ( 784-)  J  -   6.66
5222 ALA   ( 784-)  M  -   6.64
6338 ALA   ( 784-)  S  -   6.64
1881 ALA   ( 784-)  D  -   6.61
 768 ALA   ( 784-)  A  -   6.57
2996 ALA   ( 784-)  G  -   6.55
4673 GLU   ( 219-)  M  -   6.30
5785 GLU   ( 219-)  S  -   6.28
3560 GLU   ( 219-)  J  -   6.27
2442 GLU   ( 219-)  G  -   6.27
 216 GLU   ( 219-)  A  -   6.24
1330 GLU   ( 219-)  D  -   6.22
1182  ALA  ( 365-) Z  -   6.11
8529 ALA   ( 365-)  5  -   6.11
And so on for a total of 299 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 : 1.674

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.

6527 TYR   ( 150-)  T  -  15.59
4298 TYR   ( 150-)  K  -  15.58
 955 TYR   ( 150-)  B  -  15.56
5411 TYR   ( 150-)  N  -  15.51
2069 TYR   ( 150-)  E  -  15.45
3185 TYR   ( 150-)  H  -  15.36
3213 ASP   (  18-)  I  -   9.79
4326 ASP   (  18-)  L  -   9.72
5439 ASP   (  18-)  O  -   9.70
6555 ASP   (  18-)  U  -   9.70
2097 ASP   (  18-)  F  -   9.70
 983 ASP   (  18-)  C  -   9.62
2028 ASP   ( 107-)  E  -   8.29
5370 ASP   ( 107-)  N  -   8.28
4257 ASP   ( 107-)  K  -   8.25
 914 ASP   ( 107-)  B  -   8.23
6486 ASP   ( 107-)  T  -   8.18
3144 ASP   ( 107-)  H  -   8.14
4397 GLU   (  89-)  L  -   7.06
6626 GLU   (  89-)  U  -   7.02
5510 GLU   (  89-)  O  -   6.98
3284 GLU   (  89-)  I  -   6.89
1054 GLU   (  89-)  C  -   6.88
2167 GLU   (  89-)  F  -   6.67
5422 GLU   ( 161-)  N  -   5.79
And so on for a total of 108 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.

5069 PHE   ( 623-)  M  -   CB   7.05
 613 PHE   ( 623-)  A  -   CB   7.02
3961 PHE   ( 623-)  J  -   CB   7.02
1729 PHE   ( 623-)  D  -   CB   7.01
6184 PHE   ( 623-)  S  -   CB   7.00
2846 PHE   ( 623-)  G  -   CB   6.97
8163 HIS   ( 371-)  4  -   CB   5.62
8907 HIS   ( 371-)  6  -   CB   5.62
9278 HIS   ( 371-)  7  -   CB   5.60
7793 HIS   ( 371-)  3  -   CB   5.60
1183  HIS  ( 371-) Z  -    CB   5.60
7421 HIS   ( 371-)  2  -   CB   5.59
1000  HIS  ( 371-) 9  -    CB   5.59
9640 HIS   ( 371-)  8  -   CB   5.58
1037  HIS  ( 371-) V  -    CB   5.58
1146  HIS  ( 371-) Y  -    CB   5.58
8535 HIS   ( 371-)  5  -   CB   5.57
7055 HIS   ( 371-)  1  -   CB   5.57
1109  HIS  ( 371-) X  -    CB   5.57
1073  HIS  ( 371-) W  -    CB   5.56
1017  HIS  ( 173-) V  -    CB   4.19
6859 HIS   ( 173-)  1  -   CB   4.18
9448 HIS   ( 173-)  8  -   CB   4.18
7595 HIS   ( 173-)  3  -   CB   4.17
7965 HIS   ( 173-)  4  -   CB   4.17
8337 HIS   ( 173-)  5  -   CB   4.17
9811 HIS   ( 173-)  9  -   CB   4.17
8709 HIS   ( 173-)  6  -   CB   4.16
1127  HIS  ( 173-) Y  -    CB   4.16
9081 HIS   ( 173-)  7  -   CB   4.16
1054  HIS  ( 173-) W  -    CB   4.16
7226 HIS   ( 173-)  2  -   CB   4.16
1163  HIS  ( 173-) Z  -    CB   4.15
1090  HIS  ( 173-) X  -    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.

6519 PRO   ( 141-)  T  -   -2.9
3178 PRO   ( 141-)  H  -   -2.9
 948 PRO   ( 141-)  B  -   -2.9
4290 PRO   ( 141-)  K  -   -2.9
2061 PRO   ( 141-)  E  -   -2.9
5403 PRO   ( 141-)  N  -   -2.9
 813 PRO   ( 830-)  A  -   -2.9
6384 PRO   ( 830-)  S  -   -2.9
4155 PRO   ( 830-)  J  -   -2.9
3042 PRO   ( 830-)  G  -   -2.9
1927 PRO   ( 830-)  D  -   -2.9
5268 PRO   ( 830-)  M  -   -2.9
6341 ILE   ( 787-)  S  -   -2.9
2353 TYR   ( 129-)  G  -   -2.8
5696 TYR   ( 129-)  S  -   -2.8
4583 TYR   ( 129-)  M  -   -2.8
1240 TYR   ( 129-)  D  -   -2.8
 126 TYR   ( 129-)  A  -   -2.8
3470 TYR   ( 129-)  J  -   -2.8
1120  PRO  ( 109-) Y  -   -2.8
7901 PRO   ( 109-)  4  -   -2.8
8273 PRO   ( 109-)  5  -   -2.8
7531 PRO   ( 109-)  3  -   -2.8
1011  PRO  ( 109-) V  -   -2.8
1084  PRO  ( 109-) X  -   -2.8
And so on for a total of 664 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 414 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
2559 SER   ( 336-)  G  -   0.33
4790 SER   ( 336-)  M  -   0.33
5902 SER   ( 336-)  S  -   0.33
 156 SER   ( 159-)  A  -   0.36
1270 SER   ( 159-)  D  -   0.36
2383 SER   ( 159-)  G  -   0.36
3500 SER   ( 159-)  J  -   0.36
4613 SER   ( 159-)  M  -   0.36
5726 SER   ( 159-)  S  -   0.36
 416 SER   ( 420-)  A  -   0.37
1529 SER   ( 420-)  D  -   0.37
2643 SER   ( 420-)  G  -   0.37
3758 SER   ( 420-)  J  -   0.37
4870 SER   ( 420-)  M  -   0.37
5983 SER   ( 420-)  S  -   0.37
6965 SER   ( 281-)  1  -   0.40
7333 SER   ( 281-)  2  -   0.40
7703 SER   ( 281-)  3  -   0.40
8073 SER   ( 281-)  4  -   0.40
8445 SER   ( 281-)  5  -   0.40
8817 SER   ( 281-)  6  -   0.40
9189 SER   ( 281-)  7  -   0.40
9556 SER   ( 281-)  8  -   0.40
9918 SER   ( 281-)  9  -   0.40
1028  SER  ( 281-) V  -   0.40
1064  SER  ( 281-) W  -   0.40
1101  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 4630 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!

2291 GLY   (  67-)  G  -  2.50   80
3408 GLY   (  67-)  J  -  2.50   80
1178 GLY   (  67-)  D  -  2.50   80
5634 GLY   (  67-)  S  -  2.50   80
4521 GLY   (  67-)  M  -  2.50   80
  64 GLY   (  67-)  A  -  2.50   80
2752 PRO   ( 529-)  G  -  2.29   11
1638 PRO   ( 529-)  D  -  2.29   11
 523 PRO   ( 529-)  A  -  2.29   11
3867 PRO   ( 529-)  J  -  2.29   11
4979 PRO   ( 529-)  M  -  2.29   11
6092 PRO   ( 529-)  S  -  2.29   11
5846 PRO   ( 280-)  S  -  2.20   10
4734 PRO   ( 280-)  M  -  2.20   10
3621 PRO   ( 280-)  J  -  2.20   10
2503 PRO   ( 280-)  G  -  2.20   10
1391 PRO   ( 280-)  D  -  2.20   10
 277 PRO   ( 280-)  A  -  2.20   10
1517 GLY   ( 407-)  D  -  2.03   16
 403 GLY   ( 407-)  A  -  2.03   16
2630 GLY   ( 407-)  G  -  2.03   16
6194 GLY   ( 635-)  S  -  1.94   10
8310 GLY   ( 146-)  5  -  1.59   80
1087  GLY  ( 146-) X  -  1.59   80
6832 GLY   ( 146-)  1  -  1.58   80
7568 GLY   ( 146-)  3  -  1.58   80
8682 GLY   ( 146-)  6  -  1.58   80
7938 GLY   ( 146-)  4  -  1.58   80
1124  GLY  ( 146-) Y  -  1.58   80
9054 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
  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
 656 PRO   ( 669-)  A  -   0.13 LOW
 664 PRO   ( 677-)  A  -   0.02 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  -  156.4 half-chair C-alpha/N (162 degrees)
 948 PRO   ( 141-)  B  - -160.1 half-chair N/C-delta (-162 degrees)
1006 PRO   (  41-)  C  -  -10.3 half-chair C-alpha/N (-18 degrees)
1264 PRO   ( 153-)  D  -  171.6 envelop N (180 degrees)
1927 PRO   ( 830-)  D  -  156.4 half-chair C-alpha/N (162 degrees)
2061 PRO   ( 141-)  E  - -160.3 half-chair N/C-delta (-162 degrees)
2120 PRO   (  41-)  F  -  -10.5 half-chair C-alpha/N (-18 degrees)
2377 PRO   ( 153-)  G  -  171.6 envelop N (180 degrees)
3042 PRO   ( 830-)  G  -  156.7 half-chair C-alpha/N (162 degrees)
3178 PRO   ( 141-)  H  - -159.7 half-chair N/C-delta (-162 degrees)
3236 PRO   (  41-)  I  -  -10.8 half-chair C-alpha/N (-18 degrees)
3494 PRO   ( 153-)  J  -  171.5 envelop N (180 degrees)
4155 PRO   ( 830-)  J  -  156.5 half-chair C-alpha/N (162 degrees)
4290 PRO   ( 141-)  K  - -160.3 half-chair N/C-delta (-162 degrees)
4349 PRO   (  41-)  L  -  -10.4 half-chair C-alpha/N (-18 degrees)
4607 PRO   ( 153-)  M  -  171.6 envelop N (180 degrees)
5268 PRO   ( 830-)  M  -  156.8 half-chair C-alpha/N (162 degrees)
5403 PRO   ( 141-)  N  - -160.4 half-chair N/C-delta (-162 degrees)
5462 PRO   (  41-)  O  -  -10.4 half-chair C-alpha/N (-18 degrees)
5720 PRO   ( 153-)  S  -  171.6 envelop N (180 degrees)
6384 PRO   ( 830-)  S  -  156.7 half-chair C-alpha/N (162 degrees)
6519 PRO   ( 141-)  T  - -160.3 half-chair N/C-delta (-162 degrees)
6578 PRO   (  41-)  U  -  -10.3 half-chair C-alpha/N (-18 degrees)
6795 PRO   ( 109-)  1  -  112.4 envelop C-beta (108 degrees)
7163 PRO   ( 109-)  2  -  112.3 envelop C-beta (108 degrees)
7531 PRO   ( 109-)  3  -  112.3 envelop C-beta (108 degrees)
7901 PRO   ( 109-)  4  -  112.3 envelop C-beta (108 degrees)
8273 PRO   ( 109-)  5  -  112.4 envelop C-beta (108 degrees)
8645 PRO   ( 109-)  6  -  112.4 envelop C-beta (108 degrees)
9017 PRO   ( 109-)  7  -  112.3 envelop C-beta (108 degrees)
9386 PRO   ( 109-)  8  -  112.3 envelop C-beta (108 degrees)
9748 PRO   ( 109-)  9  -  112.4 envelop C-beta (108 degrees)
1011  PRO  ( 109-) V  -  112.4 envelop C-beta (108 degrees)
1047  PRO  ( 109-) W  -  112.3 envelop C-beta (108 degrees)
1084  PRO  ( 109-) X  -  112.4 envelop C-beta (108 degrees)
1120  PRO  ( 109-) Y  -  112.3 envelop C-beta (108 degrees)
1157  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.

2041 LEU   ( 121-)  E  -   CD1  <->  2048 PHE   ( 128-)  E  -   CD2  2.62    0.58  INTRA
 928 LEU   ( 121-)  B  -   CD1  <->   935 PHE   ( 128-)  B  -   CD2  2.62    0.58  INTRA
3158 LEU   ( 121-)  H  -   CD1  <->  3165 PHE   ( 128-)  H  -   CD2  2.62    0.58  INTRA
6499 LEU   ( 121-)  T  -   CD1  <->  6506 PHE   ( 128-)  T  -   CD2  2.62    0.58  INTRA
5383 LEU   ( 121-)  N  -   CD1  <->  5390 PHE   ( 128-)  N  -   CD2  2.61    0.59  INTRA
4271 LEU   ( 121-)  K  -   CD1  <->  4278 PHE   ( 128-)  K  -   CD2  2.61    0.59  INTRA
2860 LYS   ( 642-)  G  -   CE   <->  1034  SER  ( 344-) V  -    CB   2.46    0.74  INTRA
1743 LYS   ( 642-)  D  -   CE   <->  9980 SER   ( 344-)  9  -   CB   2.45    0.75  INTRA
5084 LYS   ( 642-)  M  -   CE   <->  1180  SER  ( 344-) Z  -    CB   2.45    0.75  INTRA
5399 TRP   ( 137-)  N  -   CH2  <->  5407 GLY   ( 146-)  N  -   N    2.29    0.81  INTRA
2057 TRP   ( 137-)  E  -   CH2  <->  2065 GLY   ( 146-)  E  -   N    2.29    0.81  INTRA
6515 TRP   ( 137-)  T  -   CH2  <->  6523 GLY   ( 146-)  T  -   N    2.29    0.81  INTRA
 944 TRP   ( 137-)  B  -   CH2  <->   952 GLY   ( 146-)  B  -   N    2.29    0.81  INTRA
3174 TRP   ( 137-)  H  -   CH2  <->  3182 GLY   ( 146-)  H  -   N    2.29    0.81  INTRA
5000 MLY   ( 553-)  M  -   N    <->  7101 MET   (  47-)  2  -   CA   2.24    0.86  INTRA
5080 LYS   ( 637-)  M  -   C    <->  1180  ILE  ( 345-) Z  -    CD1  2.21    0.99  INTRA
1101  LYS  ( 291-) X  -    CB   <->  1170  ASP  ( 244-) Z  -    CB   2.19    1.01  INTRA
1737 GLY   ( 632-)  D  -   C    <->  9664 ASP   (  25-)  9  -   N    2.19    0.91  INTRA
1326 GLN   ( 215-)  D  -   CD   <->  1450 ILE   ( 340-)  D  -   N    2.12    0.98  INTRA
4669 GLN   ( 215-)  M  -   CD   <->  4793 ILE   ( 340-)  M  -   N    2.12    0.98  INTRA
3556 GLN   ( 215-)  J  -   CD   <->  3680 ILE   ( 340-)  J  -   N    2.12    0.98  INTRA
 212 GLN   ( 215-)  A  -   CD   <->   336 ILE   ( 340-)  A  -   N    2.11    0.99  INTRA
6117 ASP   ( 556-)  S  -   OD2  <->  7835 GLN   (  41-)  4  -   NE2  2.09    0.61  INTRA
1660 MLY   ( 553-)  D  -   CH2  <->  1041  VAL  (  45-) W  -    CG2  2.09    1.11  INTRA
5000 MLY   ( 553-)  M  -   CH2  <->  7100 VAL   (  45-)  2  -   CG2  2.08    1.12  INTRA
And so on for a total of 8457 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: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

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.

4327 ARG   (  19-)  L  -     -7.74
6556 ARG   (  19-)  U  -     -7.74
 984 ARG   (  19-)  C  -     -7.72
5440 ARG   (  19-)  O  -     -7.70
3214 ARG   (  19-)  I  -     -7.70
1150  GLN  (  41-) Z  -     -7.52
7096 GLN   (  41-)  2  -     -7.52
8577 GLN   (  41-)  6  -     -7.51
1077  GLN  (  41-) X  -     -7.51
9680 GLN   (  41-)  9  -     -7.51
8949 GLN   (  41-)  7  -     -7.51
1041  GLN  (  41-) W  -     -7.51
9318 GLN   (  41-)  8  -     -7.51
8205 GLN   (  41-)  5  -     -7.51
1114  GLN  (  41-) Y  -     -7.51
1004  GLN  (  41-) V  -     -7.51
6727 GLN   (  41-)  1  -     -7.51
7463 GLN   (  41-)  3  -     -7.51
5696 TYR   ( 129-)  S  -     -7.41
3470 TYR   ( 129-)  J  -     -7.41
 126 TYR   ( 129-)  A  -     -7.41
1240 TYR   ( 129-)  D  -     -7.41
4583 TYR   ( 129-)  M  -     -7.41
2353 TYR   ( 129-)  G  -     -7.40
2098 ARG   (  19-)  F  -     -7.35
And so on for a total of 334 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)  -      -4.78
1682 GLU   ( 576-)  D  -   1684 - HIS    578- ( D)  -      -4.28
2372 ARG   ( 148-)  G  -   2374 - GLU    150- ( G)  -      -4.71
2799 GLU   ( 576-)  G  -   2801 - HIS    578- ( G)  -      -4.28
2924 ARG   ( 708-)  G  -   2926 - GLY    710- ( G)  -      -4.61
3489 ARG   ( 148-)  J  -   3491 - GLU    150- ( J)  -      -4.71
3914 GLU   ( 576-)  J  -   3916 - HIS    578- ( J)  -      -4.26
4602 ARG   ( 148-)  M  -   4604 - GLU    150- ( M)  -      -4.80
5022 GLU   ( 576-)  M  -   5024 - HIS    578- ( M)  -      -4.28
6137 GLU   ( 576-)  S  -   6139 - HIS    578- ( S)  -      -4.27
6725 ARG   (  39-)  1  -   6727 - GLN     41- ( 1)  -      -6.73
7094 ARG   (  39-)  2  -   7096 - GLN     41- ( 2)  -      -6.75
7461 ARG   (  39-)  3  -   7463 - GLN     41- ( 3)  -      -6.75
7833 ARG   (  39-)  4  -   7835 - GLN     41- ( 4)  -      -6.63
8203 ARG   (  39-)  5  -   8205 - GLN     41- ( 5)  -      -6.73
8575 ARG   (  39-)  6  -   8577 - GLN     41- ( 6)  -      -6.73
8947 ARG   (  39-)  7  -   8949 - GLN     41- ( 7)  -      -6.73
9316 ARG   (  39-)  8  -   9318 - GLN     41- ( 8)  -      -6.72
9678 ARG   (  39-)  9  -   9680 - GLN     41- ( 9)  -      -6.72
1004  ARG  (  39-) V  -    1004 -  GLN    41- (V ) -       -6.72
1041  ARG  (  39-) W  -    1041 -  GLN    41- (W ) -       -6.72
1077  ARG  (  39-) X  -    1077 -  GLN    41- (X ) -       -6.75
1113  ARG  (  39-) Y  -    1114 -  GLN    41- (Y ) -       -6.72
1150  ARG  (  39-) Z  -    1150 -  GLN    41- (Z ) -       -6.70

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: S

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: T

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: U

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
2085 ALA   (   6-)  F  -  -3.14
3201 ALA   (   6-)  I  -  -3.14
8576 HIS   (  40-)  6  -  -2.88
1223 ALA   ( 112-)  D  -  -2.88
5679 ALA   ( 112-)  S  -  -2.88
4566 ALA   ( 112-)  M  -  -2.88
 109 ALA   ( 112-)  A  -  -2.88
3453 ALA   ( 112-)  J  -  -2.88
1084  PRO  ( 109-) X  -  -2.87
1011  PRO  ( 109-) V  -  -2.85
1157  PRO  ( 109-) Z  -  -2.85
1120  PRO  ( 109-) Y  -  -2.85
6795 PRO   ( 109-)  1  -  -2.85
1047  PRO  ( 109-) W  -  -2.85
7163 PRO   ( 109-)  2  -  -2.85
8204 HIS   (  40-)  5  -  -2.82
5411 TYR   ( 150-)  N  -  -2.68
2069 TYR   ( 150-)  E  -  -2.68
6527 TYR   ( 150-)  T  -  -2.68
1810 GLY   ( 710-)  D  -  -2.65
3729 LEU   ( 389-)  J  -  -2.62
2612 LEU   ( 389-)  G  -  -2.62
4842 LEU   ( 389-)  M  -  -2.62
 385 LEU   ( 389-)  A  -  -2.62
5955 LEU   ( 389-)  S  -  -2.61
1499 LEU   ( 389-)  D  -  -2.61
1573 ILE   ( 464-)  D  -  -2.61
3802 ILE   ( 464-)  J  -  -2.61
4914 ILE   ( 464-)  M  -  -2.61
6027 ILE   ( 464-)  S  -  -2.61
 460 ILE   ( 464-)  A  -  -2.61
2687 ILE   ( 464-)  G  -  -2.61
9703 ILE   (  64-)  9  -  -2.61
9341 ILE   (  64-)  8  -  -2.60
8972 ILE   (  64-)  7  -  -2.58
 146 GLN   ( 149-)  A  -  -2.53
1007  ILE  (  64-) V  -  -2.52
 934 ARG   ( 127-)  B  -  -2.52
8855 ALA   ( 319-)  6  -  -2.50

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
2818 TRP   ( 595-)  G  -  - 2821 MLY   ( 598-)  G  -   -251.22
3052 PRO   ( 840-)  G  -  - 3055 LYS   ( 843-)  G  -     -1.92
3933 TRP   ( 595-)  J  -  - 3936 MLY   ( 598-)  J  -   -251.21
4165 PRO   ( 840-)  J  -  - 4168 LYS   ( 843-)  J  -     -1.84
5041 TRP   ( 595-)  M  -  - 5044 MLY   ( 598-)  M  -   -251.21
5081 GLY   ( 639-)  M  -  - 5085 GLY   ( 643-)  M  -     -1.69
5278 PRO   ( 840-)  M  -  - 5281 LYS   ( 843-)  M  -     -1.92
6156 TRP   ( 595-)  S  -  - 6159 MLY   ( 598-)  S  -   -251.21
6394 PRO   ( 840-)  S  -  - 6397 LYS   ( 843-)  S  -     -1.89
1183  ILE  ( 369-) Z  -   - 1183  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: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

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  -
1238 ASN   ( 127-)  D  -
1590 ASN   ( 481-)  D  -
1697 ASN   ( 591-)  D  -
1758 ASN   ( 658-)  D  -
2351 ASN   ( 127-)  G  -
2704 ASN   ( 481-)  G  -
2814 ASN   ( 591-)  G  -
2874 ASN   ( 658-)  G  -
3468 ASN   ( 127-)  J  -
3819 ASN   ( 481-)  J  -
3929 ASN   ( 591-)  J  -
3989 ASN   ( 658-)  J  -
4019 HIS   ( 688-)  J  -
4142 GLN   ( 817-)  J  -
4581 ASN   ( 127-)  M  -
4931 ASN   ( 481-)  M  -
5037 ASN   ( 591-)  M  -
5099 ASN   ( 658-)  M  -
5129 HIS   ( 688-)  M  -
5694 ASN   ( 127-)  S  -
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
  82 TYR   (  85-)  A  -   OH
  98 ALA   ( 101-)  A  -   N
 106 ARG   ( 109-)  A  -   NH1
 109 ALA   ( 112-)  A  -   N
 110 TRP   ( 113-)  A  -   NE1
 112 ILE   ( 115-)  A  -   N
 115 TYR   ( 118-)  A  -   OH
 118 LEU   ( 121-)  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
And so on for a total of 1711 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
 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
 477 ASN   ( 481-)  A  -   OD1
 495 GLU   ( 499-)  A  -   OE1
 579 ASP   ( 589-)  A  -   OD2
 589 ASN   ( 599-)  A  -   OD1
 642 GLU   ( 655-)  A  -   OE2
 675 HIS   ( 688-)  A  -   ND1
 685 ASN   ( 698-)  A  -   OD1
 706 ASP   ( 719-)  A  -   OD1
 843 ASP   (  35-)  B  -   OD1
 844 GLN   (  36-)  B  -   OE1
1022 GLU   (  57-)  C  -   OE2
1060 ASP   (  95-)  C  -   OD2
1197 ASP   (  86-)  D  -   OD2
1207 HIS   (  96-)  D  -   ND1
1209 HIS   (  98-)  D  -   ND1
And so on for a total of 331 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
 833 GLU   (  25-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
 834 ASP   (  26-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 837 GLU   (  29-)  B  -  H-bonding suggests Gln
 843 ASP   (  35-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 857 GLU   (  49-)  B  -  H-bonding suggests Gln
 873 ASP   (  65-)  B  -  H-bonding suggests Asn
 894 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 232 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 :  -1.869
  2nd generation packing quality :  -1.951
  Ramachandran plot appearance   :  -4.486 (bad)
  chi-1/chi-2 rotamer normality  :  -4.604 (bad)
  Backbone conformation          :  -1.040

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.960
  Bond angles                    :   1.538
  Omega angle restraints         :   0.750
  Side chain planarity           :   1.478
  Improper dihedral distribution :   1.851 (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                   :   0.960
  Bond angles                    :   1.538
  Omega angle restraints         :   0.750
  Side chain planarity           :   1.478
  Improper dihedral distribution :   1.851 (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.