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 pdb1o1d.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 : 7.470
CA-only RMS fit for the two chains : 7.463

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 : 12.370
CA-only RMS fit for the two chains : 12.401

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 : 17.300
CA-only RMS fit for the two chains : 17.349

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 : 7.065
CA-only RMS fit for the two chains : 7.027

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 : 10.358
CA-only RMS fit for the two chains : 10.387

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

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 1
Number of matrices in space group: 1
Highest polymer chain multiplicity in structure: 14
Highest polymer chain multiplicity according to SEQRES: 14
There is also strong SEQRES evidence for a multiplicity of: 14
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 12
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 14

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= 24.067
Vm by authors and this calculated Vm do not agree very well
And remember, a matrix counting problem has been reported earlier already

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  -
 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  -
 816 ASN   ( 819-)  A  -
 933 SER   ( 111-)  B  -
 949 ARG   ( 127-)  B  -
 959 TRP   ( 137-)  B  -
 987 LYS   (   4-)  C  -
1026 ASN   (  43-)  C  -
1344 GLN   ( 215-)  D  -
1537 VAL   ( 408-)  D  -
1538 GLY   ( 409-)  D  -
1672 PRO   ( 543-)  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: 0

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: 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 267 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: 0

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: 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.

 985 ARG   (  19-)  C  -
1001 ARG   (  35-)  C  -
1058 ARG   (  92-)  C  -
1074 ARG   ( 108-)  C  -
2098 ARG   (  19-)  F  -
2114 ARG   (  35-)  F  -
2170 ARG   (  92-)  F  -
2186 ARG   ( 108-)  F  -
3212 ARG   (  19-)  I  -
3228 ARG   (  35-)  I  -
3285 ARG   (  92-)  I  -
3301 ARG   ( 108-)  I  -
4325 ARG   (  19-)  L  -
4341 ARG   (  35-)  L  -
4398 ARG   (  92-)  L  -
4414 ARG   ( 108-)  L  -
5438 ARG   (  19-)  O  -
5454 ARG   (  35-)  O  -
5511 ARG   (  92-)  O  -
5527 ARG   ( 108-)  O  -
6555 ARG   (  19-)  R  -
6571 ARG   (  35-)  R  -
6627 ARG   (  92-)  R  -
6643 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

 956 TYR   ( 150-)  B  -
1105 TYR   ( 139-)  C  -
2069 TYR   ( 150-)  E  -
2217 TYR   ( 139-)  F  -
3183 TYR   ( 150-)  H  -
3332 TYR   ( 139-)  I  -
4296 TYR   ( 150-)  K  -
4445 TYR   ( 139-)  L  -
5409 TYR   ( 150-)  N  -
5558 TYR   ( 139-)  O  -
6526 TYR   ( 150-)  Q  -
6674 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.

 840 PHE   (  31-)  B  -
 889 PHE   (  80-)  B  -
 909 PHE   ( 101-)  B  -
 924 PHE   ( 116-)  B  -
 948 PHE   ( 140-)  B  -
 980 PHE   (  14-)  C  -
 983 PHE   (  17-)  C  -
1031 PHE   (  65-)  C  -
1053 PHE   (  87-)  C  -
1060 PHE   (  94-)  C  -
1953 PHE   (  31-)  E  -
2002 PHE   (  80-)  E  -
2023 PHE   ( 101-)  E  -
2037 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  -
3066 PHE   (  31-)  H  -
3115 PHE   (  80-)  H  -
3136 PHE   ( 101-)  H  -
3151 PHE   ( 116-)  H  -
3175 PHE   ( 140-)  H  -
And so on for a total of 60 lines.

Warning: Aspartic acid convention problem

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

 829 ASP   (  20-)  B  -
 835 ASP   (  26-)  B  -
 854 ASP   (  45-)  B  -
 855 ASP   (  46-)  B  -
 903 ASP   (  95-)  B  -
 955 ASP   ( 149-)  B  -
 968 ASP   ( 162-)  B  -
 974 ASP   (   8-)  C  -
 998 ASP   (  32-)  C  -
1052 ASP   (  86-)  C  -
1061 ASP   (  95-)  C  -
1942 ASP   (  20-)  E  -
1948 ASP   (  26-)  E  -
1967 ASP   (  45-)  E  -
1968 ASP   (  46-)  E  -
2017 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  -
3055 ASP   (  20-)  H  -
3061 ASP   (  26-)  H  -
3080 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.

 832 GLU   (  23-)  B  -
 834 GLU   (  25-)  B  -
 838 GLU   (  29-)  B  -
 858 GLU   (  49-)  B  -
 879 GLU   (  70-)  B  -
 895 GLU   (  86-)  B  -
 978 GLU   (  12-)  C  -
1033 GLU   (  67-)  C  -
1051 GLU   (  85-)  C  -
1055 GLU   (  89-)  C  -
1072 GLU   ( 106-)  C  -
1082 GLU   ( 116-)  C  -
1086 GLU   ( 120-)  C  -
1087 GLU   ( 121-)  C  -
1097 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    4.3
  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     1.24   -4.3
 215 LEU   ( 218-)  A  -   CB   CG    1.69    7.8
 216 GLU   ( 219-)  A  -   N   -C     1.21   -5.8
 238 ASP   ( 241-)  A  -   CG   OD1   1.34    4.7
 285 PHE   ( 288-)  A  -   CA   C     1.44   -4.1
 298 ASP   ( 301-)  A  -   CG   OD1   1.33    4.0
 303 THR   ( 306-)  A  -   CB   OG1   1.36   -4.5
 324 ASP   ( 327-)  A  -   CG   OD1   1.33    4.3
 327 GLU   ( 330-)  A  -   CD   OE1   1.33    4.1
 342 ASP   ( 346-)  A  -   CG   OD2   1.33    4.4
 343 GLU   ( 347-)  A  -   CD   OE1   1.33    4.3
 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 416 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

 |  1.002166  0.000037  0.000005|
 |  0.000037  1.002098 -0.000022|
 |  0.000005 -0.000022  1.001669|
Proposed new scale matrix

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

    A    = 300.680  B   = 300.659  C    = 300.531
    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: 1473.875
(Under-)estimated Z-score: 28.294

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  118.54    4.4
  35 VAL   (  38-)  A  -   N    CA   CB  102.72   -4.6
  44 PHE   (  47-)  A  -   C    CA   CB  101.00   -4.8
  68 THR   (  71-)  A  -   N    CA   CB  117.32    4.0
  72 ASP   (  75-)  A  -   N    CA   CB  122.96    7.3
  72 ASP   (  75-)  A  -   C    CA   CB  117.74    4.0
  79 PRO   (  82-)  A  -   N    CA   CB  109.31    5.7
  85 ILE   (  88-)  A  -   CB   CG1  CD1 101.54   -5.8
  95 HIS   (  98-)  A  -   C    CA   CB   87.30  -12.0
  95 HIS   (  98-)  A  -   CD2  CG   ND1 110.41    4.3
 101 TYR   ( 104-)  A  -   C    CA   CB  117.84    4.1
 115 TYR   ( 118-)  A  -   C    CA   CB  101.42   -4.6
 125 PRO   ( 128-)  A  -   N    CA   CB  108.10    4.6
 134 PRO   ( 137-)  A  -  -CA  -C    N   108.46   -5.6
 138 LEU   ( 141-)  A  -   C    CA   CB   97.92   -6.4
 150 PRO   ( 153-)  A  -   N    CA   CB  107.49    4.1
 158 ASN   ( 161-)  A  -   CA   CB   CG  107.55   -5.0
 158 ASN   ( 161-)  A  -   ND2  CG   OD1 127.35    4.8
 162 PHE   ( 165-)  A  -   N    CA   CB  100.37   -6.0
 162 PHE   ( 165-)  A  -   CA   CB   CG  108.75   -5.0
 169 ASN   ( 172-)  A  -   N    CA   CB  118.18    4.5
 170 GLN   ( 173-)  A  -   N    CA   CB  102.97   -4.4
 177 GLU   ( 180-)  A  -   N    CA   CB  118.53    4.7
 189 VAL   ( 192-)  A  -   CA   CB   CG1 101.97   -5.0
 193 PHE   ( 196-)  A  -   CA   CB   CG  108.22   -5.6
And so on for a total of 3096 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.

 829 ASP   (  20-)  B  -
 832 GLU   (  23-)  B  -
 834 GLU   (  25-)  B  -
 835 ASP   (  26-)  B  -
 838 GLU   (  29-)  B  -
 854 ASP   (  45-)  B  -
 855 ASP   (  46-)  B  -
 858 GLU   (  49-)  B  -
 879 GLU   (  70-)  B  -
 895 GLU   (  86-)  B  -
 903 ASP   (  95-)  B  -
 955 ASP   ( 149-)  B  -
 968 ASP   ( 162-)  B  -
 974 ASP   (   8-)  C  -
 978 GLU   (  12-)  C  -
 985 ARG   (  19-)  C  -
 998 ASP   (  32-)  C  -
1001 ARG   (  35-)  C  -
1033 GLU   (  67-)  C  -
1051 GLU   (  85-)  C  -
1052 ASP   (  86-)  C  -
1055 GLU   (  89-)  C  -
1058 ARG   (  92-)  C  -
1061 ASP   (  95-)  C  -
1072 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     9.19    33.73
  95 HIS   (  98-)  A  -   CA     8.3    49.43    34.11
  95 HIS   (  98-)  A  -   C      8.6    12.98     0.15
 134 PRO   ( 137-)  A  -   N      6.1    17.60    -2.48
 261 ASP   ( 264-)  A  -   CA     7.8    49.29    33.73
 337 LEU   ( 341-)  A  -   CA    -8.6    21.10    34.19
 443 GLN   ( 447-)  A  -   CA   -12.3    10.24    33.96
 476 ILE   ( 480-)  A  -   CB     6.6    40.86    32.31
 616 THR   ( 625-)  A  -   CB     6.5    48.73    34.09
 619 GLY   ( 628-)  A  -   C     -6.2    -8.15     0.06
 627 LYS   ( 637-)  A  -   C    -17.5   -26.31     0.11
 636 THR   ( 648-)  A  -   CB   -13.7     3.44    34.09
 637 VAL   ( 649-)  A  -   C      7.9    10.96     0.15
 637 VAL   ( 649-)  A  -   CB   -35.1   -78.98   -32.96
 686 ASN   ( 698-)  A  -   C     -6.1    -9.27     0.27
 742 THR   ( 756-)  A  -   CA     6.6    44.84    33.84
 748 HIS   ( 762-)  A  -   CA    -7.2    20.90    34.11
 816 MET   ( 832-)  A  -   CA    -7.5    20.61    34.17
 824 PRO   ( 840-)  A  -   N     -6.2   -22.82    -2.48
 830 GLU   (  21-)  B  -   C      6.5     9.44    -0.03
 831 THR   (  22-)  B  -   C      7.4    11.40     0.30
 833 ILE   (  24-)  B  -   C      6.3     8.34     0.03
 854 ASP   (  45-)  B  -   C      6.3     9.69    -0.01
 861 ALA   (  52-)  B  -   C      6.2     9.59     0.08
 870 ASN   (  61-)  B  -   C      6.6    10.67     0.27
And so on for a total of 307 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.

8120 ARG   ( 335-)  3  -   7.43
1179  ARG  ( 335-) Z  -   7.41
1142  ARG  ( 335-) Y  -   7.41
8492 ARG   ( 335-)  4  -   7.40
7012 ARG   ( 335-)  0  -   7.39
1069  ARG  ( 335-) W  -   7.39
9234 ARG   ( 335-)  7  -   7.39
7748 ARG   ( 335-)  2  -   7.38
8863 ARG   ( 335-)  5  -   7.38
7379 ARG   ( 335-)  1  -   7.38
1105  ARG  ( 335-) X  -   7.38
5220 ALA   ( 784-)  M  -   6.75
6337 ALA   ( 784-)  P  -   6.69
4108 ALA   ( 784-)  J  -   6.65
1881 ALA   ( 784-)  D  -   6.63
 770 ALA   ( 784-)  A  -   6.59
2995 ALA   ( 784-)  G  -   6.51
4670 GLU   ( 219-)  M  -   6.30
3558 GLU   ( 219-)  J  -   6.29
2441 GLU   ( 219-)  G  -   6.28
5783 GLU   ( 219-)  P  -   6.27
1331 GLU   ( 219-)  D  -   6.22
 216 GLU   ( 219-)  A  -   6.21
1145  ALA  ( 365-) Y  -   6.10
9993 ALA   ( 365-)  9  -   6.10
And so on for a total of 295 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.

6526 TYR   ( 150-)  Q  -  15.57
3183 TYR   ( 150-)  H  -  15.57
 956 TYR   ( 150-)  B  -  15.55
4296 TYR   ( 150-)  K  -  15.54
5409 TYR   ( 150-)  N  -  15.50
2069 TYR   ( 150-)  E  -  15.27
4324 ASP   (  18-)  L  -   9.76
6554 ASP   (  18-)  R  -   9.72
2097 ASP   (  18-)  F  -   9.70
3211 ASP   (  18-)  I  -   9.68
5437 ASP   (  18-)  O  -   9.67
 984 ASP   (  18-)  C  -   9.60
2029 ASP   ( 107-)  E  -   8.33
4255 ASP   ( 107-)  K  -   8.22
 915 ASP   ( 107-)  B  -   8.21
3142 ASP   ( 107-)  H  -   8.19
5368 ASP   ( 107-)  N  -   8.16
6485 ASP   ( 107-)  Q  -   8.15
6624 GLU   (  89-)  R  -   7.02
5508 GLU   (  89-)  O  -   7.01
4395 GLU   (  89-)  L  -   6.99
1055 GLU   (  89-)  C  -   6.88
3282 GLU   (  89-)  I  -   6.79
2167 GLU   (  89-)  F  -   6.75
6537 GLU   ( 161-)  Q  -   5.83
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.

 614 PHE   ( 623-)  A  -   CB   7.04
3959 PHE   ( 623-)  J  -   CB   7.00
1730 PHE   ( 623-)  D  -   CB   6.99
5067 PHE   ( 623-)  M  -   CB   6.99
6182 PHE   ( 623-)  P  -   CB   6.98
2845 PHE   ( 623-)  G  -   CB   6.97
1036  HIS  ( 371-) V  -    CB   5.61
8528 HIS   ( 371-)  4  -   CB   5.61
8899 HIS   ( 371-)  5  -   CB   5.59
8156 HIS   ( 371-)  3  -   CB   5.59
1145  HIS  ( 371-) Y  -    CB   5.59
9270 HIS   ( 371-)  7  -   CB   5.58
7047 HIS   ( 371-)  0  -   CB   5.58
9632 HIS   ( 371-)  8  -   CB   5.58
1109  HIS  ( 371-) X  -    CB   5.58
7784 HIS   ( 371-)  2  -   CB   5.57
7415 HIS   ( 371-)  1  -   CB   5.57
9999 HIS   ( 371-)  9  -   CB   5.56
1072  HIS  ( 371-) W  -    CB   5.55
1182  HIS  ( 371-) Z  -    CB   5.55
8330 HIS   ( 173-)  4  -   CB   4.19
1126  HIS  ( 173-) Y  -    CB   4.18
7219 HIS   ( 173-)  1  -   CB   4.18
1089  HIS  ( 173-) X  -    CB   4.18
9073 HIS   ( 173-)  7  -   CB   4.18
9803 HIS   ( 173-)  9  -   CB   4.17
1017  HIS  ( 173-) V  -    CB   4.17
1163  HIS  ( 173-) Z  -    CB   4.17
8702 HIS   ( 173-)  5  -   CB   4.17
6853 HIS   ( 173-)  0  -   CB   4.17
1053  HIS  ( 173-) W  -    CB   4.16
7958 HIS   ( 173-)  3  -   CB   4.16
7588 HIS   ( 173-)  2  -   CB   4.15
9440 HIS   ( 173-)  8  -   CB   4.14
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.489

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 : -4.489

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.

6518 PRO   ( 141-)  Q  -   -2.9
 949 PRO   ( 141-)  B  -   -2.9
2061 PRO   ( 141-)  E  -   -2.9
5401 PRO   ( 141-)  N  -   -2.9
3176 PRO   ( 141-)  H  -   -2.9
4288 PRO   ( 141-)  K  -   -2.9
1927 PRO   ( 830-)  D  -   -2.9
3040 PRO   ( 830-)  G  -   -2.9
6383 PRO   ( 830-)  P  -   -2.9
5266 PRO   ( 830-)  M  -   -2.9
 814 PRO   ( 830-)  A  -   -2.9
4153 PRO   ( 830-)  J  -   -2.9
 126 TYR   ( 129-)  A  -   -2.8
5694 TYR   ( 129-)  P  -   -2.8
4580 TYR   ( 129-)  M  -   -2.8
2353 TYR   ( 129-)  G  -   -2.8
3468 TYR   ( 129-)  J  -   -2.8
1241 TYR   ( 129-)  D  -   -2.8
1047  PRO  ( 109-) W  -   -2.8
6791 PRO   ( 109-)  0  -   -2.8
1083  PRO  ( 109-) X  -   -2.8
9740 PRO   ( 109-)  9  -   -2.8
7155 PRO   ( 109-)  1  -   -2.8
7894 PRO   ( 109-)  3  -   -2.8
1010  PRO  ( 109-) V  -   -2.8
And so on for a total of 654 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
 502 GLY   ( 507-)  A  - Poor phi/psi
 551 GLY   ( 560-)  A  - Poor phi/psi
 563 LYS   ( 572-)  A  - Poor phi/psi
 568 ALA   ( 577-)  A  - omega poor
 637 VAL   ( 649-)  A  - omega poor
 638 SER   ( 650-)  A  - Poor phi/psi
And so on for a total of 410 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 : -4.606

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
2558 SER   ( 336-)  G  -   0.33
 156 SER   ( 159-)  A  -   0.36
1271 SER   ( 159-)  D  -   0.36
2382 SER   ( 159-)  G  -   0.36
3498 SER   ( 159-)  J  -   0.36
4610 SER   ( 159-)  M  -   0.36
5724 SER   ( 159-)  P  -   0.36
1448 SER   ( 336-)  D  -   0.37
4787 SER   ( 336-)  M  -   0.37
 416 SER   ( 420-)  A  -   0.37
1530 SER   ( 420-)  D  -   0.37
2642 SER   ( 420-)  G  -   0.37
3756 SER   ( 420-)  J  -   0.37
4867 SER   ( 420-)  M  -   0.37
5981 SER   ( 420-)  P  -   0.37
6958 SER   ( 281-)  0  -   0.40
7325 SER   ( 281-)  1  -   0.40
7696 SER   ( 281-)  2  -   0.40
8066 SER   ( 281-)  3  -   0.40
8438 SER   ( 281-)  4  -   0.40
8809 SER   ( 281-)  5  -   0.40
9181 SER   ( 281-)  7  -   0.40
9548 SER   ( 281-)  8  -   0.40
9910 SER   ( 281-)  9  -   0.40
1027  SER  ( 281-) V  -   0.40
1063  SER  ( 281-) W  -   0.40
1100  SER  ( 281-) X  -   0.40
1137  SER  ( 281-) Y  -   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 4640 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!

3406 GLY   (  67-)  J  -  2.50   80
4518 GLY   (  67-)  M  -  2.50   80
2291 GLY   (  67-)  G  -  2.50   80
1179 GLY   (  67-)  D  -  2.50   80
  64 GLY   (  67-)  A  -  2.50   80
5632 GLY   (  67-)  P  -  2.50   80
2751 PRO   ( 529-)  G  -  2.29   11
1639 PRO   ( 529-)  D  -  2.29   11
 524 PRO   ( 529-)  A  -  2.29   11
6090 PRO   ( 529-)  P  -  2.29   11
3865 PRO   ( 529-)  J  -  2.29   11
4976 PRO   ( 529-)  M  -  2.29   11
3619 PRO   ( 280-)  J  -  2.20   10
4731 PRO   ( 280-)  M  -  2.20   10
5844 PRO   ( 280-)  P  -  2.20   10
2502 PRO   ( 280-)  G  -  2.20   10
1392 PRO   ( 280-)  D  -  2.20   10
 277 PRO   ( 280-)  A  -  2.20   10
1518 GLY   ( 407-)  D  -  2.03   16
2629 GLY   ( 407-)  G  -  2.03   16
 403 GLY   ( 407-)  A  -  2.03   16
6192 GLY   ( 635-)  P  -  1.94   10
8675 GLY   ( 146-)  5  -  1.59   80
7192 GLY   ( 146-)  1  -  1.59   80
7931 GLY   ( 146-)  3  -  1.58   80
1123  GLY  ( 146-) Y  -  1.58   80
7561 GLY   ( 146-)  2  -  1.58   80
1086  GLY  ( 146-) X  -  1.58   80
9046 GLY   ( 146-)  7  -  1.58   80
8303 GLY   ( 146-)  4  -  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  -   0.11 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
 524 PRO   ( 529-)  A  -   0.13 LOW
 537 PRO   ( 543-)  A  -   0.06 LOW
 559 PRO   ( 568-)  A  -   0.02 LOW
 561 PRO   ( 570-)  A  -   0.07 LOW
 593 PRO   ( 602-)  A  -   0.04 LOW
 657 PRO   ( 669-)  A  -   0.13 LOW
 665 PRO   ( 677-)  A  -   0.02 LOW
 671 PRO   ( 683-)  A  -   0.10 LOW
And so on for a total of 283 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)
 814 PRO   ( 830-)  A  -  156.2 half-chair C-alpha/N (162 degrees)
 949 PRO   ( 141-)  B  - -159.9 half-chair N/C-delta (-162 degrees)
1007 PRO   (  41-)  C  -  -10.3 half-chair C-alpha/N (-18 degrees)
1265 PRO   ( 153-)  D  -  171.4 envelop N (180 degrees)
1927 PRO   ( 830-)  D  -  156.5 half-chair C-alpha/N (162 degrees)
2061 PRO   ( 141-)  E  - -160.4 half-chair N/C-delta (-162 degrees)
2120 PRO   (  41-)  F  -  -10.8 half-chair C-alpha/N (-18 degrees)
2376 PRO   ( 153-)  G  -  171.7 envelop N (180 degrees)
3040 PRO   ( 830-)  G  -  156.7 half-chair C-alpha/N (162 degrees)
3176 PRO   ( 141-)  H  - -159.6 half-chair N/C-delta (-162 degrees)
3234 PRO   (  41-)  I  -  -10.9 half-chair C-alpha/N (-18 degrees)
3492 PRO   ( 153-)  J  -  171.4 envelop N (180 degrees)
4153 PRO   ( 830-)  J  -  156.7 half-chair C-alpha/N (162 degrees)
4288 PRO   ( 141-)  K  - -160.6 half-chair N/C-delta (-162 degrees)
4347 PRO   (  41-)  L  -  -10.7 half-chair C-alpha/N (-18 degrees)
4604 PRO   ( 153-)  M  -  171.7 envelop N (180 degrees)
5266 PRO   ( 830-)  M  -  156.6 half-chair C-alpha/N (162 degrees)
5401 PRO   ( 141-)  N  - -160.4 half-chair N/C-delta (-162 degrees)
5460 PRO   (  41-)  O  -  -10.2 half-chair C-alpha/N (-18 degrees)
5718 PRO   ( 153-)  P  -  171.6 envelop N (180 degrees)
6383 PRO   ( 830-)  P  -  156.8 half-chair C-alpha/N (162 degrees)
6518 PRO   ( 141-)  Q  - -160.3 half-chair N/C-delta (-162 degrees)
6577 PRO   (  41-)  R  -  -10.4 half-chair C-alpha/N (-18 degrees)
6791 PRO   ( 109-)  0  -  112.4 envelop C-beta (108 degrees)
7155 PRO   ( 109-)  1  -  112.2 envelop C-beta (108 degrees)
7524 PRO   ( 109-)  2  -  112.3 envelop C-beta (108 degrees)
7894 PRO   ( 109-)  3  -  112.3 envelop C-beta (108 degrees)
8266 PRO   ( 109-)  4  -  112.3 envelop C-beta (108 degrees)
8638 PRO   ( 109-)  5  -  112.4 envelop C-beta (108 degrees)
9009 PRO   ( 109-)  7  -  112.3 envelop C-beta (108 degrees)
9378 PRO   ( 109-)  8  -  112.3 envelop C-beta (108 degrees)
9740 PRO   ( 109-)  9  -  112.3 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  -  112.3 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.

2042 LEU   ( 121-)  E  -   CD1  <->  2048 PHE   ( 128-)  E  -   CD2  2.62    0.58  INTRA
 929 LEU   ( 121-)  B  -   CD1  <->   936 PHE   ( 128-)  B  -   CD2  2.62    0.58  INTRA
3156 LEU   ( 121-)  H  -   CD1  <->  3163 PHE   ( 128-)  H  -   CD2  2.62    0.58  INTRA
6498 LEU   ( 121-)  Q  -   CD1  <->  6505 PHE   ( 128-)  Q  -   CD2  2.62    0.58  INTRA
4269 LEU   ( 121-)  K  -   CD1  <->  4276 PHE   ( 128-)  K  -   CD2  2.62    0.58  INTRA
5381 LEU   ( 121-)  N  -   CD1  <->  5388 PHE   ( 128-)  N  -   CD2  2.61    0.59  INTRA
2859 LYS   ( 642-)  G  -   CE   <->  1033  SER  ( 344-) V  -    CB   2.46    0.74  INTRA
1744 LYS   ( 642-)  D  -   CE   <->  9972 SER   ( 344-)  9  -   CB   2.45    0.75  INTRA
5082 LYS   ( 642-)  M  -   CE   <->  1180  SER  ( 344-) Z  -    CB   2.45    0.75  INTRA
6199 LYS   ( 642-)  P  -   CE   <->  7021 SER   ( 344-)  0  -   CB   2.45    0.75  INTRA
5397 TRP   ( 137-)  N  -   CH2  <->  5405 GLY   ( 146-)  N  -   N    2.29    0.81  INTRA
6514 TRP   ( 137-)  Q  -   CH2  <->  6522 GLY   ( 146-)  Q  -   N    2.29    0.81  INTRA
 945 TRP   ( 137-)  B  -   CH2  <->   953 GLY   ( 146-)  B  -   N    2.29    0.81  INTRA
2057 TRP   ( 137-)  E  -   CH2  <->  2065 GLY   ( 146-)  E  -   N    2.29    0.81  INTRA
3172 TRP   ( 137-)  H  -   CH2  <->  3180 GLY   ( 146-)  H  -   N    2.29    0.81  INTRA
5078 LYS   ( 637-)  M  -   C    <->  1180  ILE  ( 345-) Z  -    CD1  2.21    0.99  INTRA
1738 GLY   ( 632-)  D  -   C    <->  9656 ASP   (  25-)  9  -   N    2.19    0.91  INTRA
4993 THR   ( 548-)  M  -   CG2  <->  7094 MET   (  47-)  1  -   SD   2.13    1.27  INTRA
3554 GLN   ( 215-)  J  -   CD   <->  3678 ILE   ( 340-)  J  -   N    2.12    0.98  INTRA
4666 GLN   ( 215-)  M  -   CD   <->  4790 ILE   ( 340-)  M  -   N    2.12    0.98  INTRA
1327 GLN   ( 215-)  D  -   CD   <->  1451 ILE   ( 340-)  D  -   N    2.12    0.98  INTRA
 212 GLN   ( 215-)  A  -   CD   <->   336 ILE   ( 340-)  A  -   N    2.11    0.99  INTRA
1661 MLY   ( 553-)  D  -   CH2  <->  1040  VAL  (  45-) W  -    CG2  2.09    1.11  INTRA
2317 MET   (  93-)  G  -   CG   <->  2929 ARG   ( 714-)  G  -   O    2.08    0.72  INTRA
5018 LYS   ( 574-)  M  -   NZ   <->  5033 ASP   ( 589-)  M  -   OD2  2.06    0.64  INTRA
And so on for a total of 8415 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: 0

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: 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.

7089 GLN   (  41-)  1  -     -7.76
4325 ARG   (  19-)  L  -     -7.73
 985 ARG   (  19-)  C  -     -7.72
6555 ARG   (  19-)  R  -     -7.71
3212 ARG   (  19-)  I  -     -7.71
5438 ARG   (  19-)  O  -     -7.71
2098 ARG   (  19-)  F  -     -7.54
1004  GLN  (  41-) V  -     -7.52
9310 GLN   (  41-)  8  -     -7.51
8570 GLN   (  41-)  5  -     -7.51
1113  GLN  (  41-) Y  -     -7.51
1150  GLN  (  41-) Z  -     -7.51
1040  GLN  (  41-) W  -     -7.51
9672 GLN   (  41-)  9  -     -7.51
8941 GLN   (  41-)  7  -     -7.51
6723 GLN   (  41-)  0  -     -7.51
8198 GLN   (  41-)  4  -     -7.51
7826 GLN   (  41-)  3  -     -7.51
1076  GLN  (  41-) X  -     -7.51
5694 TYR   ( 129-)  P  -     -7.42
3468 TYR   ( 129-)  J  -     -7.41
 126 TYR   ( 129-)  A  -     -7.41
4580 TYR   ( 129-)  M  -     -7.41
2353 TYR   ( 129-)  G  -     -7.40
1241 TYR   ( 129-)  D  -     -7.40
And so on for a total of 328 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.

 567 GLU   ( 576-)  A  -    569 - HIS    578- ( A)  -      -4.28
1260 ARG   ( 148-)  D  -   1262 - GLU    150- ( D)  -      -4.77
1683 GLU   ( 576-)  D  -   1685 - HIS    578- ( D)  -      -4.28
2798 GLU   ( 576-)  G  -   2800 - HIS    578- ( G)  -      -4.27
2923 ARG   ( 708-)  G  -   2925 - GLY    710- ( G)  -      -4.60
3487 ARG   ( 148-)  J  -   3489 - GLU    150- ( J)  -      -4.65
3912 GLU   ( 576-)  J  -   3914 - HIS    578- ( J)  -      -4.26
4599 ARG   ( 148-)  M  -   4601 - GLU    150- ( M)  -      -4.65
5020 GLU   ( 576-)  M  -   5022 - HIS    578- ( M)  -      -4.27
6135 GLU   ( 576-)  P  -   6137 - HIS    578- ( P)  -      -4.27
6264 ARG   ( 708-)  P  -   6266 - GLY    710- ( P)  -      -4.61
6721 ARG   (  39-)  0  -   6723 - GLN     41- ( 0)  -      -6.74
7087 ARG   (  39-)  1  -   7089 - GLN     41- ( 1)  -      -6.82
7455 ARG   (  39-)  2  -   7457 - GLN     41- ( 2)  -      -5.59
7824 ARG   (  39-)  3  -   7826 - GLN     41- ( 3)  -      -6.73
8196 ARG   (  39-)  4  -   8198 - GLN     41- ( 4)  -      -6.72
8568 ARG   (  39-)  5  -   8570 - GLN     41- ( 5)  -      -6.73
8939 ARG   (  39-)  7  -   8941 - GLN     41- ( 7)  -      -6.73
9308 ARG   (  39-)  8  -   9310 - GLN     41- ( 8)  -      -6.72
9670 ARG   (  39-)  9  -   9672 - 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 ) -       -6.74
1113  ARG  (  39-) Y  -    1113 -  GLN    41- (Y ) -       -6.73
1149  ARG  (  39-) Z  -    1150 -  GLN    41- (Z ) -       -6.74

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: 0

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: 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.

 972 ALA   (   6-)  C  -  -3.14
2085 ALA   (   6-)  F  -  -3.14
3199 ALA   (   6-)  I  -  -3.14
1224 ALA   ( 112-)  D  -  -2.88
5677 ALA   ( 112-)  P  -  -2.88
4563 ALA   ( 112-)  M  -  -2.88
3451 ALA   ( 112-)  J  -  -2.88
1119  PRO  ( 109-) Y  -  -2.85
1010  PRO  ( 109-) V  -  -2.85
7155 PRO   ( 109-)  1  -  -2.85
1083  PRO  ( 109-) X  -  -2.85
6791 PRO   ( 109-)  0  -  -2.85
1047  PRO  ( 109-) W  -  -2.85
1156  PRO  ( 109-) Z  -  -2.85
8569 HIS   (  40-)  5  -  -2.84
2069 TYR   ( 150-)  E  -  -2.68
5409 TYR   ( 150-)  N  -  -2.68
6526 TYR   ( 150-)  Q  -  -2.67
1006  ILE  (  64-) V  -  -2.66
9695 ILE   (  64-)  9  -  -2.65
8964 ILE   (  64-)  7  -  -2.62
5953 LEU   ( 389-)  P  -  -2.62
3727 LEU   ( 389-)  J  -  -2.62
1500 LEU   ( 389-)  D  -  -2.62
 385 LEU   ( 389-)  A  -  -2.62
4839 LEU   ( 389-)  M  -  -2.62
2611 LEU   ( 389-)  G  -  -2.61
1574 ILE   ( 464-)  D  -  -2.61
6025 ILE   ( 464-)  P  -  -2.61
4911 ILE   ( 464-)  M  -  -2.61
 460 ILE   ( 464-)  A  -  -2.61
3800 ILE   ( 464-)  J  -  -2.61
9333 ILE   (  64-)  8  -  -2.58
3913 ALA   ( 577-)  J  -  -2.55
8197 HIS   (  40-)  4  -  -2.53
1811 GLY   ( 710-)  D  -  -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.

 586 TRP   ( 595-)  A  -  -  589 MLY   ( 598-)  A  -   -251.21
1702 TRP   ( 595-)  D  -  - 1705 MLY   ( 598-)  D  -   -251.21
1741 GLY   ( 639-)  D  -  - 1745 GLY   ( 643-)  D  -     -1.69
2817 TRP   ( 595-)  G  -  - 2820 MLY   ( 598-)  G  -   -251.21
3050 PRO   ( 840-)  G  -  - 3053 LYS   ( 843-)  G  -     -1.91
3931 TRP   ( 595-)  J  -  - 3934 MLY   ( 598-)  J  -   -251.21
4163 PRO   ( 840-)  J  -  - 4166 LYS   ( 843-)  J  -     -1.94
5039 TRP   ( 595-)  M  -  - 5042 MLY   ( 598-)  M  -   -251.21
5079 GLY   ( 639-)  M  -  - 5083 GLY   ( 643-)  M  -     -1.69
5276 PRO   ( 840-)  M  -  - 5279 LYS   ( 843-)  M  -     -1.95
6154 TRP   ( 595-)  P  -  - 6157 MLY   ( 598-)  P  -   -251.21
6197 LYS   ( 640-)  P  -  - 6200 GLY   ( 643-)  P  -     -2.01
6393 PRO   ( 840-)  P  -  - 6396 LYS   ( 843-)  P  -     -1.95
1182  ILE  ( 369-) Z  -   - 1182  ARG  ( 372-) Z  -      -1.72
ERROR. Too many residues to use DSSP

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: 0

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: 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.

 124 ASN   ( 127-)  A  -
 477 ASN   ( 481-)  A  -
 582 ASN   ( 591-)  A  -
 646 ASN   ( 658-)  A  -
1239 ASN   ( 127-)  D  -
1591 ASN   ( 481-)  D  -
1698 ASN   ( 591-)  D  -
1759 ASN   ( 658-)  D  -
2351 ASN   ( 127-)  G  -
2703 ASN   ( 481-)  G  -
2813 ASN   ( 591-)  G  -
2873 ASN   ( 658-)  G  -
3466 ASN   ( 127-)  J  -
3817 ASN   ( 481-)  J  -
3927 ASN   ( 591-)  J  -
3987 ASN   ( 658-)  J  -
4017 HIS   ( 688-)  J  -
4578 ASN   ( 127-)  M  -
4928 ASN   ( 481-)  M  -
5035 ASN   ( 591-)  M  -
5097 ASN   ( 658-)  M  -
5692 ASN   ( 127-)  P  -
6042 ASN   ( 481-)  P  -
6150 ASN   ( 591-)  P  -
6214 ASN   ( 658-)  P  -
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
 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
 138 LEU   ( 141-)  A  -   N
And so on for a total of 1683 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
 495 GLU   ( 499-)  A  -   OE1
 580 ASP   ( 589-)  A  -   OD2
 590 ASN   ( 599-)  A  -   OD1
 643 GLU   ( 655-)  A  -   OE2
 676 HIS   ( 688-)  A  -   ND1
 686 ASN   ( 698-)  A  -   OD1
 707 ASP   ( 719-)  A  -   OD1
 844 ASP   (  35-)  B  -   OD1
 845 GLN   (  36-)  B  -   OE1
 955 ASP   ( 149-)  B  -   OD1
 967 GLU   ( 161-)  B  -   OE1
1023 GLU   (  57-)  C  -   OE2
1061 ASP   (  95-)  C  -   OD2
1198 ASP   (  86-)  D  -   OD2
1208 HIS   (  96-)  D  -   ND1
And so on for a total of 319 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
 533 GLU   ( 539-)  A  -  H-bonding suggests Gln
 596 GLU   ( 605-)  A  -  H-bonding suggests Gln
 707 ASP   ( 719-)  A  -  H-bonding suggests Asn
 793 GLU   ( 808-)  A  -  H-bonding suggests Gln
 834 GLU   (  25-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
 835 ASP   (  26-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 838 GLU   (  29-)  B  -  H-bonding suggests Gln
 844 ASP   (  35-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 858 GLU   (  49-)  B  -  H-bonding suggests Gln
 874 ASP   (  65-)  B  -  H-bonding suggests Asn
 895 GLU   (  86-)  B  -  H-bonding suggests Gln
 900 ASP   (  92-)  B  -  H-bonding suggests Asn
 913 ASP   ( 105-)  B  -  H-bonding suggests Asn
 927 GLU   ( 119-)  B  -  H-bonding suggests Gln
 955 ASP   ( 149-)  B  -  H-bonding suggests Asn
 978 GLU   (  12-)  C  -  H-bonding suggests Gln; but Alt-Rotamer
 984 ASP   (  18-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
1055 GLU   (  89-)  C  -  H-bonding suggests Gln
1061 ASP   (  95-)  C  -  H-bonding suggests Asn
1090 GLU   ( 124-)  C  -  H-bonding suggests Gln
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 :  -1.872
  2nd generation packing quality :  -1.946
  Ramachandran plot appearance   :  -4.489 (bad)
  chi-1/chi-2 rotamer normality  :  -4.606 (bad)
  Backbone conformation          :  -1.028

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.961
  Bond angles                    :   1.538
  Omega angle restraints         :   0.751
  Side chain planarity           :   1.479
  Improper dihedral distribution :   1.857 (loose)
  B-factor distribution          :   0.362
  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                   :   0.961
  Bond angles                    :   1.538
  Omega angle restraints         :   0.751
  Side chain planarity           :   1.479
  Improper dihedral distribution :   1.857 (loose)
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.012
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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Bond lengths and angles, DNA/RNA
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DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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      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.