WHAT IF Check report

This file was created 2013-12-10 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 pdb4hhh.ent

Checks that need to be done early-on in validation

Warning: Nonstandard space group setting

The space group name given represents a non-standard setting.

Space group name: P 21 2 21

Conventional space group : P 21 21 2

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 109.790  B   = 109.950  C    = 201.440
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 109.790  B   = 109.950  C    = 201.440
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 109.950  B   = 109.790  C    = 201.440
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 21 2 21

Bravais type of conventional cell is: P

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 B

All-atom RMS fit for the two chains : 0.875
CA-only RMS fit for the two chains : 0.468

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 B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.865
CA-only RMS fit for the two chains : 0.450

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.759
CA-only RMS fit for the two chains : 0.426

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: B and C

All-atom RMS fit for the two chains : 0.786
CA-only RMS fit for the two chains : 0.437

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.851
CA-only RMS fit for the two chains : 0.499

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2329 RUB   ( 501-)  A  -
2330 RUB   ( 501-)  B  -
2331 RUB   ( 501-)  C  -
2332 RUB   ( 501-)  D  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

1874 LEU   (  42-)  S  -
2236 ARG   (  35-)  V  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

1874 LEU   (  42-)  S  -
2236 ARG   (  35-)  V  -

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: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Coordinate problems, unexpected atoms, B-factor and occupancy checks

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 54.12

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

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.

 868 ARG   ( 421-)  B
1404 ARG   (  41-)  D
1723 ARG   ( 360-)  D
2055 ARG   ( 100-)  T

Warning: Tyrosine convention problem

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

  13 TYR   (  24-)  A
  74 TYR   (  85-)  A
  92 TYR   ( 103-)  A
 131 TYR   ( 142-)  A
 174 TYR   ( 185-)  A
 258 TYR   ( 269-)  A
 272 TYR   ( 283-)  A
 352 TYR   ( 363-)  A
 716 TYR   ( 269-)  B
 810 TYR   ( 363-)  B
 985 TYR   (  80-)  C
1174 TYR   ( 269-)  C
1188 TYR   ( 283-)  C
1268 TYR   ( 363-)  C
1463 TYR   ( 100-)  D
1466 TYR   ( 103-)  D
1505 TYR   ( 142-)  D
1632 TYR   ( 269-)  D
1646 TYR   ( 283-)  D
1716 TYR   ( 353-)  D
1726 TYR   ( 363-)  D
1849 TYR   (  17-)  S
1884 TYR   (  52-)  S
1893 TYR   (  61-)  S
1972 TYR   (  17-)  T
2007 TYR   (  52-)  T
2016 TYR   (  61-)  T
2017 TYR   (  62-)  T
2078 TYR   ( 123-)  T
2095 TYR   (  17-)  U
2130 TYR   (  52-)  U
2201 TYR   ( 123-)  U
2218 TYR   (  17-)  V
2253 TYR   (  52-)  V
2262 TYR   (  61-)  V

Warning: Phenylalanine convention problem

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

 114 PHE   ( 125-)  A
 137 PHE   ( 148-)  A
 207 PHE   ( 218-)  A
 263 PHE   ( 274-)  A
 458 PHE   ( 469-)  A
 544 PHE   (  97-)  B
 572 PHE   ( 125-)  B
 595 PHE   ( 148-)  B
 658 PHE   ( 211-)  B
 665 PHE   ( 218-)  B
 792 PHE   ( 345-)  B
 916 PHE   ( 469-)  B
 945 PHE   (  40-)  C
1002 PHE   (  97-)  C
1030 PHE   ( 125-)  C
1032 PHE   ( 127-)  C
1053 PHE   ( 148-)  C
1123 PHE   ( 218-)  C
1299 PHE   ( 394-)  C
1403 PHE   (  40-)  D
1480 PHE   ( 117-)  D
1488 PHE   ( 125-)  D
1511 PHE   ( 148-)  D
1708 PHE   ( 345-)  D
1765 PHE   ( 402-)  D
1832 PHE   ( 469-)  D
1844 PHE   (  12-)  S
1876 PHE   (  44-)  S
1930 PHE   (  98-)  S
1947 PHE   ( 115-)  S
1999 PHE   (  44-)  T
2005 PHE   (  50-)  T
2090 PHE   (  12-)  U
2122 PHE   (  44-)  U
2176 PHE   (  98-)  U
2193 PHE   ( 115-)  U
2245 PHE   (  44-)  V
2251 PHE   (  50-)  V
2299 PHE   (  98-)  V
2316 PHE   ( 115-)  V

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.

 425 ASP   ( 436-)  A
 814 ASP   ( 367-)  B
 883 ASP   ( 436-)  B
 999 ASP   (  94-)  C
1108 ASP   ( 203-)  C
1272 ASP   ( 367-)  C
1341 ASP   ( 436-)  C
1500 ASP   ( 137-)  D
1730 ASP   ( 367-)  D
1799 ASP   ( 436-)  D
2034 ASP   (  79-)  T

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.

  40 GLU   (  51-)  A
  41 GLU   (  52-)  A
  75 GLU   (  86-)  A
  82 GLU   (  93-)  A
 147 GLU   ( 158-)  A
 220 GLU   ( 231-)  A
 325 GLU   ( 336-)  A
 327 GLU   ( 338-)  A
 429 GLU   ( 440-)  A
 453 GLU   ( 464-)  A
 457 GLU   ( 468-)  A
 533 GLU   (  86-)  B
 535 GLU   (  88-)  B
 678 GLU   ( 231-)  B
 783 GLU   ( 336-)  B
 785 GLU   ( 338-)  B
 839 GLU   ( 392-)  B
 915 GLU   ( 468-)  B
 991 GLU   (  86-)  C
 998 GLU   (  93-)  C
1014 GLU   ( 109-)  C
1041 GLU   ( 136-)  C
1063 GLU   ( 158-)  C
1136 GLU   ( 231-)  C
1164 GLU   ( 259-)  C
1241 GLU   ( 336-)  C
1245 GLU   ( 340-)  C
1345 GLU   ( 440-)  C
1369 GLU   ( 464-)  C
1414 GLU   (  51-)  D
1415 GLU   (  52-)  D
1423 GLU   (  60-)  D
1449 GLU   (  86-)  D
1451 GLU   (  88-)  D
1456 GLU   (  93-)  D
1472 GLU   ( 109-)  D
1699 GLU   ( 336-)  D
1803 GLU   ( 440-)  D
1831 GLU   ( 468-)  D
1861 GLU   (  29-)  S
1886 GLU   (  54-)  S
1921 GLU   (  89-)  S
1925 GLU   (  93-)  S
2041 GLU   (  86-)  T
2048 GLU   (  93-)  T
2132 GLU   (  54-)  U
2214 GLU   (  13-)  V
2255 GLU   (  54-)  V
2290 GLU   (  89-)  V

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.

  94 LEU   ( 105-)  A      CA   C     1.43   -4.4
 115 GLY   ( 126-)  A      N    CA    1.52    4.0
 142 HIS   ( 153-)  A      N    CA    1.56    5.1
 189 THR   ( 200-)  A      CA   C     1.61    4.2
 194 ASN   ( 205-)  A      CA   CB    1.64    5.5
 199 PRO   ( 210-)  A      C    O     1.31    4.1
 203 TRP   ( 214-)  A      CG   CD2   1.53    5.1
 203 TRP   ( 214-)  A      NE1  CE2   1.28   -7.9
 225 LYS   ( 236-)  A      CA   C     1.63    4.9
 229 LEU   ( 240-)  A      CA   C     1.61    4.3
 250 GLY   ( 261-)  A      N    CA    1.53    5.0
 257 ASP   ( 268-)  A      CA   C     1.62    4.4
 271 HIS   ( 282-)  A      CG   CD2   1.42    5.6
 271 HIS   ( 282-)  A      ND1  CE1   1.38    5.0
 296 HIS   ( 307-)  A      CG   CD2   1.41    4.6
 299 HIS   ( 310-)  A      CG   CD2   1.40    4.1
 305 LYS   ( 316-)  A      N    CA    1.54    4.2
 362 GLY   ( 373-)  A      N    CA    1.56    6.5
 372 HIS   ( 383-)  A      CG   CD2   1.41    4.5
 389 LEU   ( 400-)  A      N    CA    1.54    4.3
 569 GLY   ( 122-)  B      N    CA    1.52    4.4
 634 ARG   ( 187-)  B      CA   CB    1.43   -4.8
 661 TRP   ( 214-)  B      N    CA    1.54    4.5
 661 TRP   ( 214-)  B      CD2  CE2   1.48    4.1
 685 HIS   ( 238-)  B      CG   CD2   1.41    4.5
And so on for a total of 63 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

 |  0.993905 -0.000134 -0.000161|
 | -0.000134  0.997722  0.000482|
 | -0.000161  0.000482  0.996268|
Proposed new scale matrix

 |  0.009164  0.000001  0.000001|
 |  0.000001  0.009116 -0.000004|
 |  0.000000 -0.000002  0.004983|
With corresponding cell

    A    = 109.124  B   = 109.700  C    = 200.699
    Alpha=  89.945  Beta=  90.010  Gamma=  90.015

The CRYST1 cell dimensions

    A    = 109.790  B   = 109.950  C    = 201.440
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1346.620
(Under-)estimated Z-score: 27.045

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.

  30 ARG   (  41-)  A      CG   CD   NE  103.12   -4.3
  83 ASP   (  94-)  A     -C    N    CA  131.21    5.3
 111 GLY   ( 122-)  A      N    CA   C   124.23    4.0
 115 GLY   ( 126-)  A     -C    N    CA  130.22    5.7
 120 ARG   ( 131-)  A      CD   NE   CZ  129.09    4.1
 121 ALA   ( 132-)  A     -C    N    CA  113.78   -4.4
 124 LEU   ( 135-)  A      CB   CG   CD1 123.62    4.3
 128 ARG   ( 139-)  A      CG   CD   NE  117.81    4.3
 142 HIS   ( 153-)  A      CG   ND1  CE1 110.55    5.0
 147 GLU   ( 158-)  A     -C    N    CA  114.15   -4.2
 161 CYS   ( 172-)  A      CA   CB   SG  124.12    4.2
 173 ASN   ( 184-)  A      C    CA   CB  102.29   -4.1
 176 ARG   ( 187-)  A      CG   CD   NE  121.65    6.6
 178 VAL   ( 189-)  A      N    CA   C    99.03   -4.3
 194 ASN   ( 205-)  A     -C    N    CA  130.22    4.7
 195 VAL   ( 206-)  A      C    CA   CB   98.94   -5.9
 206 ARG   ( 217-)  A      CG   CD   NE  121.03    6.2
 210 CYS   ( 221-)  A      CA   CB   SG  102.48   -5.2
 219 ALA   ( 230-)  A      C    CA   CB  103.85   -4.4
 227 HIS   ( 238-)  A      CG   ND1  CE1 110.00    4.4
 229 LEU   ( 240-)  A      CB   CG   CD1 123.27    4.2
 242 ARG   ( 253-)  A      CG   CD   NE  102.72   -4.6
 247 ARG   ( 258-)  A      CG   CD   NE   95.87   -8.6
 248 GLU   ( 259-)  A      N    CA   C   124.25    4.7
 255 MET   ( 266-)  A      N    CA   CB  102.63   -4.6
And so on for a total of 160 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.

  40 GLU   (  51-)  A
  41 GLU   (  52-)  A
  75 GLU   (  86-)  A
  82 GLU   (  93-)  A
 147 GLU   ( 158-)  A
 220 GLU   ( 231-)  A
 325 GLU   ( 336-)  A
 327 GLU   ( 338-)  A
 425 ASP   ( 436-)  A
 429 GLU   ( 440-)  A
 453 GLU   ( 464-)  A
 457 GLU   ( 468-)  A
 533 GLU   (  86-)  B
 535 GLU   (  88-)  B
 678 GLU   ( 231-)  B
 783 GLU   ( 336-)  B
 785 GLU   ( 338-)  B
 814 ASP   ( 367-)  B
 839 GLU   ( 392-)  B
 868 ARG   ( 421-)  B
 883 ASP   ( 436-)  B
 915 GLU   ( 468-)  B
 991 GLU   (  86-)  C
 998 GLU   (  93-)  C
 999 ASP   (  94-)  C
And so on for a total of 64 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.

 130 PRO   ( 141-)  A      N      6.7    19.63    -2.48
 554 LEU   ( 107-)  B      C     -6.2    -9.56     0.20
 862 PRO   ( 415-)  B      N     -6.5   -23.93    -2.48
1046 PRO   ( 141-)  C      N      6.6    19.23    -2.48
1060 ILE   ( 155-)  C      CB     6.4    40.62    32.31
1632 TYR   ( 269-)  D      CA    -6.0    24.49    34.03
The average deviation= 1.680

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.

 248 GLU   ( 259-)  A    8.52
 178 VAL   ( 189-)  A    7.62
 872 GLU   ( 425-)  B    7.46
1505 TYR   ( 142-)  D    7.28
 602 ILE   ( 155-)  B    6.84
1632 TYR   ( 269-)  D    6.46
1709 VAL   ( 346-)  D    6.42
1224 ARG   ( 319-)  C    6.35
 291 ASP   ( 302-)  A    6.15
1662 ALA   ( 299-)  D    6.05
 764 ALA   ( 317-)  B    5.95
1295 LEU   ( 390-)  C    5.91
 985 TYR   (  80-)  C    5.91
 717 LEU   ( 270-)  B    5.90
 505 ALA   (  58-)  B    5.82
 190 LYS   ( 201-)  A    5.78
 891 ILE   ( 444-)  B    5.75
  69 TYR   (  80-)  A    5.66
1776 ASN   ( 413-)  D    5.61
1131 TYR   ( 226-)  C    5.60
 726 THR   ( 279-)  B    5.54
 836 ALA   ( 389-)  B    5.51
 636 VAL   ( 189-)  B    5.50
 267 THR   ( 278-)  A    5.43
  96 LEU   ( 107-)  A    5.43
And so on for a total of 98 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 : 1.886

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.

1182 ASN   ( 277-)  C    8.57
 584 ASP   ( 137-)  B    5.83
 316 HIS   ( 327-)  A    5.23
1657 HIS   ( 294-)  D    5.09
 275 ASP   ( 286-)  A    4.71
1191 ASP   ( 286-)  C    4.57
 238 GLU   ( 249-)  A    4.46
 714 HIS   ( 267-)  B    4.43
1011 ASP   ( 106-)  C    4.27
1192 ASN   ( 287-)  C    4.25
1232 HIS   ( 327-)  C    4.14
 556 GLU   ( 109-)  B    4.07
 256 HIS   ( 267-)  A    4.05

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.774

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.

 574 PHE   ( 127-)  B    -3.5
 497 PRO   (  50-)  B    -3.1
1621 ARG   ( 258-)  D    -3.0
 955 PRO   (  50-)  C    -3.0
  39 PRO   (  50-)  A    -3.0
 493 PRO   (  46-)  B    -2.9
2206 PRO   (   5-)  V    -2.9
1274 VAL   ( 369-)  C    -2.7
 358 VAL   ( 369-)  A    -2.7
 923 LYS   (  18-)  C    -2.7
1184 THR   ( 279-)  C    -2.7
2214 GLU   (  13-)  V    -2.6
1884 TYR   (  52-)  S    -2.6
1961 PRO   (   6-)  T    -2.6
 247 ARG   ( 258-)  A    -2.6
1889 LYS   (  57-)  S    -2.6
 561 THR   ( 114-)  B    -2.6
 816 VAL   ( 369-)  B    -2.6
1169 ILE   ( 264-)  C    -2.6
2097 PRO   (  19-)  U    -2.6
 972 THR   (  67-)  C    -2.6
 970 THR   (  65-)  C    -2.6
 647 THR   ( 200-)  B    -2.6
 711 ILE   ( 264-)  B    -2.5
1541 LEU   ( 178-)  D    -2.5
And so on for a total of 140 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.

  24 ASP   (  35-)  A  omega poor
  25 ILE   (  36-)  A  omega poor
  51 SER   (  62-)  A  Poor phi/psi
  52 THR   (  63-)  A  Poor phi/psi, omega poor
  53 GLY   (  64-)  A  omega poor
  58 VAL   (  69-)  A  omega poor
  70 LYS   (  81-)  A  omega poor
  72 ARG   (  83-)  A  omega poor
  82 GLU   (  93-)  A  omega poor
  83 ASP   (  94-)  A  Poor phi/psi
  84 ASN   (  95-)  A  Poor phi/psi
  88 ALA   (  99-)  A  omega poor
  96 LEU   ( 107-)  A  omega poor
  97 PHE   ( 108-)  A  omega poor
 100 GLY   ( 111-)  A  omega poor
 107 THR   ( 118-)  A  omega poor
 111 GLY   ( 122-)  A  Poor phi/psi, omega poor
 119 LEU   ( 130-)  A  omega poor
 121 ALA   ( 132-)  A  omega poor
 136 THR   ( 147-)  A  omega poor
 152 ASN   ( 163-)  A  Poor phi/psi
 164 LYS   ( 175-)  A  PRO omega poor
 169 LEU   ( 180-)  A  omega poor
 175 GLY   ( 186-)  A  omega poor
 177 ALA   ( 188-)  A  omega poor
And so on for a total of 323 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 : -5.045

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.

 270 SER   ( 281-)  A    0.36
 675 SER   ( 228-)  B    0.37
1809 ARG   ( 446-)  D    0.38

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 ALA   (  15-)  A      0
   6 VAL   (  17-)  A      0
  12 THR   (  23-)  A      0
  13 TYR   (  24-)  A      0
  14 TYR   (  25-)  A      0
  15 THR   (  26-)  A      0
  35 PRO   (  46-)  A      0
  37 VAL   (  48-)  A      0
  50 SER   (  61-)  A      0
  51 SER   (  62-)  A      0
  52 THR   (  63-)  A      0
  55 TRP   (  66-)  A      0
  56 THR   (  67-)  A      0
  59 TRP   (  70-)  A      0
  63 LEU   (  74-)  A      0
  74 TYR   (  85-)  A      0
  80 PRO   (  91-)  A      0
  82 GLU   (  93-)  A      0
  83 ASP   (  94-)  A      0
  84 ASN   (  95-)  A      0
  85 GLN   (  96-)  A      0
  99 GLU   ( 110-)  A      0
 109 ILE   ( 120-)  A      0
 110 VAL   ( 121-)  A      0
 112 ASN   ( 123-)  A      0
And so on for a total of 933 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 9.110

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!

1700 GLY   ( 337-)  D   2.40   20
 326 GLY   ( 337-)  A   2.15   13
 784 GLY   ( 337-)  B   2.08   18
1242 GLY   ( 337-)  C   1.95   10
1234 GLY   ( 329-)  C   1.82   16
 394 GLY   ( 405-)  A   1.69   80

Warning: Unusual peptide bond conformations

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

 752 LYS   ( 305-)  B   2.03

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]

 157 PRO   ( 168-)  A    0.55 HIGH
 361 PRO   ( 372-)  A    0.48 HIGH
 496 PRO   (  49-)  B    0.11 LOW
 819 PRO   ( 372-)  B    0.03 LOW
1081 PRO   ( 176-)  C    0.46 HIGH
1115 PRO   ( 210-)  C    0.08 LOW
1168 PRO   ( 263-)  C    0.57 HIGH
1281 PRO   ( 376-)  C    0.08 LOW
1504 PRO   ( 141-)  D    0.47 HIGH
1514 PRO   ( 151-)  D    0.19 LOW
1735 PRO   ( 372-)  D    0.47 HIGH
2035 PRO   (  80-)  T    0.14 LOW

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].

  39 PRO   (  50-)  A   145.6 envelop C-alpha (144 degrees)
 130 PRO   ( 141-)  A   -34.6 envelop C-alpha (-36 degrees)
 199 PRO   ( 210-)  A   152.4 envelop C-alpha (144 degrees)
 399 PRO   ( 410-)  A  -119.9 half-chair C-delta/C-gamma (-126 degrees)
 497 PRO   (  50-)  B   173.1 envelop N (180 degrees)
 536 PRO   (  89-)  B    26.7 half-chair N/C-delta (18 degrees)
 538 PRO   (  91-)  B   101.9 envelop C-beta (108 degrees)
 623 PRO   ( 176-)  B  -125.8 half-chair C-delta/C-gamma (-126 degrees)
 835 PRO   ( 388-)  B    43.6 envelop C-delta (36 degrees)
 857 PRO   ( 410-)  B  -137.2 envelop C-delta (-144 degrees)
 862 PRO   ( 415-)  B  -151.6 envelop C-delta (-144 degrees)
 955 PRO   (  50-)  C   125.8 half-chair C-beta/C-alpha (126 degrees)
1009 PRO   ( 104-)  C    52.8 half-chair C-delta/C-gamma (54 degrees)
1046 PRO   ( 141-)  C   -20.3 half-chair C-alpha/N (-18 degrees)
1168 PRO   ( 263-)  C  -118.5 half-chair C-delta/C-gamma (-126 degrees)
1277 PRO   ( 372-)  C    34.8 envelop C-delta (36 degrees)
1315 PRO   ( 410-)  C  -124.8 half-chair C-delta/C-gamma (-126 degrees)
1358 PRO   ( 453-)  C    50.4 half-chair C-delta/C-gamma (54 degrees)
1407 PRO   (  44-)  D   -46.9 half-chair C-beta/C-alpha (-54 degrees)
1409 PRO   (  46-)  D   108.8 envelop C-beta (108 degrees)
1412 PRO   (  49-)  D   101.8 envelop C-beta (108 degrees)
1454 PRO   (  91-)  D  -156.2 half-chair N/C-delta (-162 degrees)
1515 PRO   ( 152-)  D    51.3 half-chair C-delta/C-gamma (54 degrees)
1573 PRO   ( 210-)  D  -151.2 envelop C-delta (-144 degrees)
1778 PRO   ( 415-)  D    45.4 half-chair C-delta/C-gamma (54 degrees)
1837 PRO   (   5-)  S  -155.3 half-chair N/C-delta (-162 degrees)
1905 PRO   (  73-)  S   103.7 envelop C-beta (108 degrees)
1927 PRO   (  95-)  S  -117.1 half-chair C-delta/C-gamma (-126 degrees)
1961 PRO   (   6-)  T   -48.8 half-chair C-beta/C-alpha (-54 degrees)
1995 PRO   (  40-)  T   -43.8 envelop C-alpha (-36 degrees)
2014 PRO   (  59-)  T    35.6 envelop C-delta (36 degrees)
2050 PRO   (  95-)  T    49.2 half-chair C-delta/C-gamma (54 degrees)
2075 PRO   ( 120-)  T  -138.7 envelop C-delta (-144 degrees)
2083 PRO   (   5-)  U    28.9 envelop C-delta (36 degrees)
2097 PRO   (  19-)  U   145.3 envelop C-alpha (144 degrees)
2118 PRO   (  40-)  U    52.7 half-chair C-delta/C-gamma (54 degrees)
2137 PRO   (  59-)  U   170.8 half-chair C-alpha/N (162 degrees)
2151 PRO   (  73-)  U  -134.5 half-chair C-delta/C-gamma (-126 degrees)
2206 PRO   (   5-)  V   121.3 half-chair C-beta/C-alpha (126 degrees)
2220 PRO   (  19-)  V  -119.9 half-chair C-delta/C-gamma (-126 degrees)
2221 PRO   (  20-)  V   115.5 envelop C-beta (108 degrees)
2260 PRO   (  59-)  V   104.6 envelop C-beta (108 degrees)
2281 PRO   (  80-)  V   -19.3 half-chair C-alpha/N (-18 degrees)
2296 PRO   (  95-)  V    43.8 envelop C-delta (36 degrees)
2321 PRO   ( 120-)  V    28.8 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

1106 LYS   ( 201-)  C      NZ  <-> 1199 HIS   ( 294-)  C      NE2    1.30    1.70  INTRA BL
1564 LYS   ( 201-)  D      NZ  <-> 1657 HIS   ( 294-)  D      NE2    1.02    1.98  INTRA BL
 241 LYS   ( 252-)  A      NZ  <-> 1649 ASP   ( 286-)  D      OD1    0.82    1.88  INTRA BL
 294 LYS   ( 305-)  A      N   <-> 2333 HOH   ( 753 )  A      O      0.64    2.06  INTRA BL
  85 GLN   (  96-)  A      NE2 <->  295 ASN   ( 306-)  A      OD1    0.64    2.06  INTRA BL
1657 HIS   ( 294-)  D      CE1 <-> 1690 HIS   ( 327-)  D      NE2    0.63    2.47  INTRA BL
1106 LYS   ( 201-)  C      NZ  <-> 1199 HIS   ( 294-)  C      CD2    0.62    2.48  INTRA BL
2049 TYR   (  94-)  T      OH  <-> 2338 HOH   ( 228 )  T      O      0.61    1.79  INTRA BL
 120 ARG   ( 131-)  A      CD  <-> 2333 HOH   ( 694 )  A      O      0.61    2.19  INTRA BL
1648 ARG   ( 285-)  D      NH1 <-> 2336 HOH   ( 669 )  D      O      0.61    2.09  INTRA BL
2212 LYS   (  11-)  V      NZ  <-> 2340 HOH   ( 238 )  V      O      0.60    2.10  INTRA BL
 168 GLY   ( 179-)  A      O   <-> 2310 GLN   ( 109-)  V      NE2    0.59    2.11  INTRA BL
1597 GLU   ( 234-)  D      OE1 <-> 2336 HOH   ( 667 )  D      O      0.56    1.84  INTRA BL
1191 ASP   ( 286-)  C      OD1 <-> 1615 LYS   ( 252-)  D      NZ     0.55    2.15  INTRA BL
1669 ASN   ( 306-)  D    A ND2 <-> 2336 HOH   ( 728 )  D      O      0.55    2.15  INTRA BL
1564 LYS   ( 201-)  D      CE  <-> 1657 HIS   ( 294-)  D      NE2    0.55    2.55  INTRA BL
1710 ASP   ( 347-)  D      OD2 <-> 1723 ARG   ( 360-)  D    A NH2    0.54    2.16  INTRA BL
 280 LEU   ( 291-)  A      N   <->  313 ASP   ( 324-)  A      OD2    0.54    2.16  INTRA BL
1058 HIS   ( 153-)  C      CE1 <-> 2335 HOH   ( 610 )  C      O      0.54    2.26  INTRA BL
 925 TYR   (  20-)  C      O   <->  927 LEU   (  22-)  C      N      0.54    2.16  INTRA
 948 THR   (  43-)  C      OG1 <-> 1001 GLN   (  96-)  C      NE2    0.53    2.17  INTRA BL
1272 ASP   ( 367-)  C      OD1 <-> 2335 HOH   ( 732 )  C      O      0.53    1.87  INTRA BL
2186 ARG   ( 108-)  U      NH2 <-> 2190 CYS   ( 112-)  U      SG     0.53    2.77  INTRA
 986 LYS   (  81-)  C      O   <->  988 ARG   (  83-)  C    A NH1    0.52    2.18  INTRA BL
1527 LYS   ( 164-)  D      NZ  <-> 1598 ILE   ( 235-)  D      O      0.50    2.20  INTRA BL
And so on for a total of 1090 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: 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: V

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.

 782 LEU   ( 335-)  B      -7.09
1698 LEU   ( 335-)  D      -7.00
1036 ARG   ( 131-)  C      -6.95
 324 LEU   ( 335-)  A      -6.92
1240 LEU   ( 335-)  C      -6.87
 578 ARG   ( 131-)  B      -6.86
 292 ARG   ( 303-)  A      -6.53
 120 ARG   ( 131-)  A      -6.44
1802 ARG   ( 439-)  D      -6.29
2153 PHE   (  75-)  U      -6.16
 886 ARG   ( 439-)  B      -6.13
1907 PHE   (  75-)  S      -6.07
2276 PHE   (  75-)  V      -6.06
2030 PHE   (  75-)  T      -6.06
2076 GLU   ( 121-)  T      -6.05
1494 ARG   ( 131-)  D      -6.04
2125 LYS   (  47-)  U      -6.01
1928 ARG   (  96-)  S      -5.89
 428 ARG   ( 439-)  A      -5.83
1666 ARG   ( 303-)  D      -5.81
1814 TRP   ( 451-)  D      -5.80
2002 LYS   (  47-)  T      -5.80
1344 ARG   ( 439-)  C      -5.75
 783 GLU   ( 336-)  B      -5.74
1054 GLN   ( 149-)  C      -5.73
And so on for a total of 86 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.

 323 LYS   ( 334-)  A       325 - GLU    336- ( A)         -5.66
 455 LYS   ( 466-)  A       457 - GLU    468- ( A)         -4.65
 781 LYS   ( 334-)  B       783 - GLU    336- ( B)         -5.96
1239 LYS   ( 334-)  C      1241 - GLU    336- ( C)         -5.75
1697 LYS   ( 334-)  D      1699 - GLU    336- ( D)         -5.51

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: 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: V

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.

2188 VAL   ( 110-)  U   -3.10
1385 LEU   (  22-)  D   -2.97
1342 LEU   ( 437-)  C   -2.86
 552 LEU   ( 105-)  B   -2.78
 288 ALA   ( 299-)  A   -2.73
1010 LEU   ( 105-)  C   -2.62
1204 ALA   ( 299-)  C   -2.59
 554 LEU   ( 107-)  B   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 745 HIS   ( 298-)  B     -  748 ILE   ( 301-)  B        -1.59

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: 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: V

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

2333 HOH   ( 633 )  A      O     25.31  -46.16  -25.47
2333 HOH   ( 752 )  A      O      1.07  -35.67   -9.56
2334 HOH   ( 760 )  B      O    -40.04  -76.18  -11.13
2335 HOH   ( 668 )  C      O      0.13 -110.18  -14.94
2336 HOH   ( 673 )  D      O     43.42  -83.14  -23.37

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

2333 HOH   ( 760 )  A      O

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.

 218 GLN   ( 229-)  A
 256 HIS   ( 267-)  A
 281 HIS   ( 292-)  A
 293 GLN   ( 304-)  A
 295 ASN   ( 306-)  A
 296 HIS   ( 307-)  A
 355 GLN   ( 366-)  A
 562 ASN   ( 115-)  B
 596 GLN   ( 149-)  B
 600 HIS   ( 153-)  B
 714 HIS   ( 267-)  B
 724 ASN   ( 277-)  B
 813 GLN   ( 366-)  B
1020 ASN   ( 115-)  C
1054 GLN   ( 149-)  C
1058 HIS   ( 153-)  C
1112 ASN   ( 207-)  C
1172 HIS   ( 267-)  C
1187 HIS   ( 282-)  C
1478 ASN   ( 115-)  D
1519 GLN   ( 156-)  D
1601 HIS   ( 238-)  D
1630 HIS   ( 267-)  D
1746 HIS   ( 383-)  D
1772 HIS   ( 409-)  D
1887 HIS   (  55-)  S
1950 HIS   ( 118-)  S
2060 ASN   ( 105-)  T
2160 GLN   (  82-)  U
2189 GLN   ( 111-)  U
2306 ASN   ( 105-)  V
2312 GLN   ( 111-)  V

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.

  11 LEU   (  22-)  A      N
  17 ASP   (  28-)  A      N
  56 THR   (  67-)  A      N
  56 THR   (  67-)  A      OG1
  85 GLN   (  96-)  A      N
 101 SER   ( 112-)  A      OG
 104 ASN   ( 115-)  A      ND2
 108 SER   ( 119-)  A      N
 118 ALA   ( 129-)  A      N
 123 ARG   ( 134-)  A      NE
 150 LYS   ( 161-)  A      NZ
 154 TYR   ( 165-)  A      N
 156 ARG   ( 167-)  A      N
 162 THR   ( 173-)  A      OG1
 164 LYS   ( 175-)  A      N
 164 LYS   ( 175-)  A      NZ
 167 LEU   ( 178-)  A      N
 168 GLY   ( 179-)  A      N
 174 TYR   ( 185-)  A      OH
 185 GLY   ( 196-)  A      N
 190 LYS   ( 201-)  A      NZ
 196 ASN   ( 207-)  A      ND2
 200 PHE   ( 211-)  A      N
 206 ARG   ( 217-)  A      NH1
 213 ALA   ( 224-)  A      N
And so on for a total of 268 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.

 125 GLU   ( 136-)  A    A OE1
 142 HIS   ( 153-)  A      NE2
 257 ASP   ( 268-)  A      OD1
 283 HIS   ( 294-)  A      NE2
 313 ASP   ( 324-)  A      OD2
 316 HIS   ( 327-)  A      ND1
 390 GLN   ( 401-)  A      OE1
 570 ASN   ( 123-)  B      OD1
 652 ASN   ( 205-)  B      OD1
 654 ASN   ( 207-)  B      OD1
 715 ASP   ( 268-)  B      OD1
 715 ASP   ( 268-)  B      OD2
 774 HIS   ( 327-)  B      ND1
 848 GLN   ( 401-)  B      OE1
1063 GLU   ( 158-)  C      OE1
1173 ASP   ( 268-)  C      OD1
1199 HIS   ( 294-)  C      NE2
1230 HIS   ( 325-)  C      ND1
1232 HIS   ( 327-)  C      ND1
1338 GLU   ( 433-)  C      OE2
1516 HIS   ( 153-)  D      NE2
1521 GLU   ( 158-)  D      OE1
1570 ASN   ( 207-)  D      OD1
1631 ASP   ( 268-)  D      OD1
1688 HIS   ( 325-)  D      ND1
1690 HIS   ( 327-)  D      ND1
1764 GLN   ( 401-)  D      OE1
2010 HIS   (  55-)  T      NE2
2107 GLU   (  29-)  U      OE2
2230 GLU   (  29-)  V      OE2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

2337 HOH   ( 203 )  S      O  0.90  K  4
2338 HOH   ( 225 )  T      O  0.94 NA  4

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.

 414 GLU   ( 425-)  A   H-bonding suggests Gln
 715 ASP   ( 268-)  B   H-bonding suggests Asn
 733 ASP   ( 286-)  B   H-bonding suggests Asn
 798 ASP   ( 351-)  B   H-bonding suggests Asn
 843 ASP   ( 396-)  B   H-bonding suggests Asn
1173 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1207 ASP   ( 302-)  C   H-bonding suggests Asn; but Alt-Rotamer
1330 GLU   ( 425-)  C   H-bonding suggests Gln
1423 GLU   (  60-)  D   H-bonding suggests Gln
1586 GLU   ( 223-)  D   H-bonding suggests Gln
1631 ASP   ( 268-)  D   H-bonding suggests Asn
1665 ASP   ( 302-)  D   H-bonding suggests Asn
1788 GLU   ( 425-)  D   H-bonding suggests Gln; but Alt-Rotamer
1953 GLU   ( 121-)  S   H-bonding suggests Gln; but Alt-Rotamer
2164 GLU   (  86-)  U   H-bonding suggests Gln; but Alt-Rotamer
2199 GLU   ( 121-)  U   H-bonding suggests Gln

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 :  -1.946
  2nd generation packing quality :  -1.532
  Ramachandran plot appearance   :  -3.774 (poor)
  chi-1/chi-2 rotamer normality  :  -5.045 (bad)
  Backbone conformation          :  -0.782

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.020
  Bond angles                    :   1.193
  Omega angle restraints         :   1.656 (loose)
  Side chain planarity           :   1.366
  Improper dihedral distribution :   1.420
  Inside/Outside distribution    :   1.080

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.1
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -3.4 (poor)
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.020
  Bond angles                    :   1.193
  Omega angle restraints         :   1.656 (loose)
  Side chain planarity           :   1.366
  Improper dihedral distribution :   1.420
  Inside/Outside distribution    :   1.080
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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      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.