WHAT IF Check report

This file was created 2012-01-13 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 pdb1upm.ent

Checks that need to be done early-on in validation

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    = 219.600  B   = 220.942  C    = 116.984
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 116.984  B   = 219.600  C    = 220.942
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 220.942  B   = 219.600  C    = 116.984
    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 21 2

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: B and E

All-atom RMS fit for the two chains : 0.223
CA-only RMS fit for the two chains : 0.045

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 H

All-atom RMS fit for the two chains : 0.172
CA-only RMS fit for the two chains : 0.041

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 K

All-atom RMS fit for the two chains : 0.210
CA-only RMS fit for the two chains : 0.041

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 L

All-atom RMS fit for the two chains : 0.222
CA-only RMS fit for the two chains : 0.046

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 O

All-atom RMS fit for the two chains : 0.179
CA-only RMS fit for the two chains : 0.040

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.

4730 CAP   ( 477-)  B  -
4732 CAP   ( 477-)  E  -
4734 CAP   ( 477-)  H  -
4736 CAP   ( 477-)  K  -
4738 CAP   ( 477-)  L  -
4740 CAP   ( 477-)  O  -
4742 CAP   ( 477-)  R  -
4744 CAP   ( 477-)  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: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   4 GLU   (  12-)  B      CB
   4 GLU   (  12-)  B      CG
   4 GLU   (  12-)  B      CD
   4 GLU   (  12-)  B      OE1
   4 GLU   (  12-)  B      OE2
 594 GLU   (  12-)  E      CB
 594 GLU   (  12-)  E      CG
 594 GLU   (  12-)  E      CD
 594 GLU   (  12-)  E      OE1
 594 GLU   (  12-)  E      OE2
1184 GLU   (  12-)  H      CB
1184 GLU   (  12-)  H      CG
1184 GLU   (  12-)  H      CD
1184 GLU   (  12-)  H      OE1
1184 GLU   (  12-)  H      OE2
1774 GLU   (  12-)  K      CB
1774 GLU   (  12-)  K      CG
1774 GLU   (  12-)  K      CD
1774 GLU   (  12-)  K      OE1
1774 GLU   (  12-)  K      OE2
2241 GLU   (  12-)  L      CB
2241 GLU   (  12-)  L      CG
2241 GLU   (  12-)  L      CD
2241 GLU   (  12-)  L      OE1
2241 GLU   (  12-)  L      OE2
2831 GLU   (  12-)  O      CB
2831 GLU   (  12-)  O      CG
2831 GLU   (  12-)  O      CD
2831 GLU   (  12-)  O      OE1
2831 GLU   (  12-)  O      OE2
3421 GLU   (  12-)  R      CB
3421 GLU   (  12-)  R      CG
3421 GLU   (  12-)  R      CD
3421 GLU   (  12-)  R      OE1
3421 GLU   (  12-)  R      OE2
4134 GLU   (  12-)  V      CB
4134 GLU   (  12-)  V      CG
4134 GLU   (  12-)  V      CD
4134 GLU   (  12-)  V      OE1
4134 GLU   (  12-)  V      OE2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 ALA   (   9-)  B    High
   2 SER   (  10-)  B    High
 591 ALA   (   9-)  E    High
 592 SER   (  10-)  E    High
1181 ALA   (   9-)  H    High
1182 SER   (  10-)  H    High
1771 ALA   (   9-)  K    High
1772 SER   (  10-)  K    High
2238 ALA   (   9-)  L    High
2239 SER   (  10-)  L    High
2828 ALA   (   9-)  O    High
2829 SER   (  10-)  O    High
3418 ALA   (   9-)  R    High
3419 SER   (  10-)  R    High
4131 ALA   (   9-)  V    High
4132 SER   (  10-)  V    High

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:

Crystal temperature (K) :279.000

Note: B-factor plot

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

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

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.

 427 ARG   ( 435-)  B
1017 ARG   ( 435-)  E
1607 ARG   ( 435-)  H
2197 ARG   ( 435-)  K
2664 ARG   ( 435-)  L
3254 ARG   ( 435-)  O
3844 ARG   ( 435-)  R
4557 ARG   ( 435-)  V

Warning: Tyrosine convention problem

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

  95 TYR   ( 103-)  B
 479 TYR   (  12-)  C
 529 TYR   (  62-)  C
 667 TYR   (  85-)  E
 685 TYR   ( 103-)  E
 865 TYR   ( 283-)  E
1069 TYR   (  12-)  F
1119 TYR   (  62-)  F
1180 TYR   ( 123-)  F
1275 TYR   ( 103-)  H
1455 TYR   ( 283-)  H
1709 TYR   (  62-)  I
1847 TYR   (  85-)  K
1865 TYR   ( 103-)  K
2716 TYR   (  12-)  M
2766 TYR   (  62-)  M
2827 TYR   ( 123-)  M
2922 TYR   ( 103-)  O
3356 TYR   (  62-)  P
3494 TYR   (  85-)  R
3512 TYR   ( 103-)  R
3896 TYR   (  12-)  S
4019 TYR   (  12-)  T
4130 TYR   ( 123-)  T
4207 TYR   (  85-)  V
4225 TYR   ( 103-)  V
4405 TYR   ( 283-)  V
4609 TYR   (  12-)  W
4659 TYR   (  62-)  W
4720 TYR   ( 123-)  W

Warning: Phenylalanine convention problem

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

 140 PHE   ( 148-)  B
 203 PHE   ( 211-)  B
 394 PHE   ( 402-)  B
 565 PHE   (  98-)  C
 730 PHE   ( 148-)  E
 793 PHE   ( 211-)  E
 984 PHE   ( 402-)  E
1172 PHE   ( 115-)  F
1320 PHE   ( 148-)  H
1574 PHE   ( 402-)  H
1745 PHE   (  98-)  I
1910 PHE   ( 148-)  K
1973 PHE   ( 211-)  K
2164 PHE   ( 402-)  K
2231 PHE   ( 469-)  K
2377 PHE   ( 148-)  L
2440 PHE   ( 211-)  L
2631 PHE   ( 402-)  L
2802 PHE   (  98-)  M
2819 PHE   ( 115-)  M
2967 PHE   ( 148-)  O
3030 PHE   ( 211-)  O
3221 PHE   ( 402-)  O
3392 PHE   (  98-)  P
3409 PHE   ( 115-)  P
3557 PHE   ( 148-)  R
3620 PHE   ( 211-)  R
3811 PHE   ( 402-)  R
3878 PHE   ( 469-)  R
3982 PHE   (  98-)  S
3999 PHE   ( 115-)  S
4105 PHE   (  98-)  T
4270 PHE   ( 148-)  V
4333 PHE   ( 211-)  V
4524 PHE   ( 402-)  V
4591 PHE   ( 469-)  V
4695 PHE   (  98-)  W
4712 PHE   ( 115-)  W

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.

  22 GLU   (  30-)  B
  86 GLU   (  94-)  B
 612 GLU   (  30-)  E
 676 GLU   (  94-)  E
1202 GLU   (  30-)  H
1266 GLU   (  94-)  H
1792 GLU   (  30-)  K
1856 GLU   (  94-)  K
2259 GLU   (  30-)  L
2323 GLU   (  94-)  L
2849 GLU   (  30-)  O
2913 GLU   (  94-)  O
3439 GLU   (  30-)  R
3503 GLU   (  94-)  R
4152 GLU   (  30-)  V
4216 GLU   (  94-)  V

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 193 KCX   ( 201-)  B      CH     CX
 193 KCX   ( 201-)  B      OX1    OQ1
 193 KCX   ( 201-)  B      OX2    OQ2
 783 KCX   ( 201-)  E      CH     CX
 783 KCX   ( 201-)  E      OX1    OQ1
 783 KCX   ( 201-)  E      OX2    OQ2
1373 KCX   ( 201-)  H      CH     CX
1373 KCX   ( 201-)  H      OX1    OQ1
1373 KCX   ( 201-)  H      OX2    OQ2
1963 KCX   ( 201-)  K      CH     CX
1963 KCX   ( 201-)  K      OX1    OQ1
1963 KCX   ( 201-)  K      OX2    OQ2
2430 KCX   ( 201-)  L      CH     CX
2430 KCX   ( 201-)  L      OX1    OQ1
2430 KCX   ( 201-)  L      OX2    OQ2
3020 KCX   ( 201-)  O      CH     CX
3020 KCX   ( 201-)  O      OX1    OQ1
3020 KCX   ( 201-)  O      OX2    OQ2
3610 KCX   ( 201-)  R      CH     CX
3610 KCX   ( 201-)  R      OX1    OQ1
3610 KCX   ( 201-)  R      OX2    OQ2
4323 KCX   ( 201-)  V      CH     CX
4323 KCX   ( 201-)  V      OX1    OQ1
4323 KCX   ( 201-)  V      OX2    OQ2

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.

 468 MET   (   1-)  C      N    CA    2.86   73.7
 876 HIS   ( 294-)  E      ND1  CE1   1.39    5.5
1466 HIS   ( 294-)  H      ND1  CE1   1.39    5.5
2056 HIS   ( 294-)  K      ND1  CE1   1.37    4.2
3113 HIS   ( 294-)  O      ND1  CE1   1.38    4.7
3585 PRO   ( 176-)  R      CD   N     1.59    8.6
4416 HIS   ( 294-)  V      ND1  CE1   1.38    5.0

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

 |  0.995854 -0.000155 -0.000003|
 | -0.000155  0.998948  0.000223|
 | -0.000003  0.000223  1.000683|
Proposed new scale matrix

 |  0.004573  0.000000  0.000000|
 |  0.000000  0.004531 -0.000001|
 |  0.000000 -0.000002  0.008542|
With corresponding cell

    A    = 218.677  B   = 220.713  C    = 117.066
    Alpha=  89.974  Beta=  90.002  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 219.600  B   = 220.942  C    = 116.984
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 603.569
(Under-)estimated Z-score: 18.106

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.

  18 THR   (  26-)  B      N    CA   CB  101.12   -5.5
  18 THR   (  26-)  B      C    CA   CB  120.33    5.4
  18 THR   (  26-)  B      CA   CB   CG2 119.46    5.3
  32 PHE   (  40-)  B      CA   CB   CG  119.65    5.9
  61 VAL   (  69-)  B      N    CA   CB   96.63   -8.2
  61 VAL   (  69-)  B      C    CA   CB  122.76    6.7
  61 VAL   (  69-)  B      CA   CB   CG1 118.21    4.5
  64 ASP   (  72-)  B      CA   CB   CG  116.65    4.0
  67 THR   (  75-)  B      N    CA   CB  117.52    4.1
  67 THR   (  75-)  B      C    CA   CB   99.54   -5.6
  71 ARG   (  79-)  B      CG   CD   NE  120.13    5.7
  75 ARG   (  83-)  B      CD   NE   CZ  135.36    7.6
 101 GLU   ( 109-)  B      CB   CG   CD  120.62    4.7
 113 VAL   ( 121-)  B      N    CA   CB  100.81   -5.7
 119 PHE   ( 127-)  B      CA   CB   CG  119.45    5.7
 145 HIS   ( 153-)  B      CA   CB   CG  107.78   -6.0
 159 ARG   ( 167-)  B      CD   NE   CZ  129.56    4.4
 167 LYS   ( 175-)  B      C    CA   CB  118.57    4.5
 168 PRO   ( 176-)  B     -O   -C    N   129.05    5.0
 168 PRO   ( 176-)  B      N    CA   CB  109.20    5.6
 168 PRO   ( 176-)  B      C    CA   CB  122.47    6.5
 168 PRO   ( 176-)  B      CD   N    CA   99.68   -8.8
 179 ARG   ( 187-)  B      CD   NE   CZ  129.90    4.6
 191 PHE   ( 199-)  B      CA   CB   CG  121.21    7.4
 194 ASP   ( 202-)  B      CA   CB   CG  117.41    4.8
And so on for a total of 567 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.

  22 GLU   (  30-)  B
  86 GLU   (  94-)  B
 427 ARG   ( 435-)  B
 612 GLU   (  30-)  E
 676 GLU   (  94-)  E
1017 ARG   ( 435-)  E
1202 GLU   (  30-)  H
1266 GLU   (  94-)  H
1607 ARG   ( 435-)  H
1792 GLU   (  30-)  K
1856 GLU   (  94-)  K
2197 ARG   ( 435-)  K
2259 GLU   (  30-)  L
2323 GLU   (  94-)  L
2664 ARG   ( 435-)  L
2849 GLU   (  30-)  O
2913 GLU   (  94-)  O
3254 ARG   ( 435-)  O
3439 GLU   (  30-)  R
3503 GLU   (  94-)  R
3844 ARG   ( 435-)  R
4152 GLU   (  30-)  V
4216 GLU   (  94-)  V
4557 ARG   ( 435-)  V

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.

  61 VAL   (  69-)  B      CB     9.4   -20.64   -32.96
 168 PRO   ( 176-)  B      N      8.1    24.07    -2.48
 168 PRO   ( 176-)  B      CA    -8.2    26.63    38.15
 577 VAL   ( 110-)  C      CB     7.7   -22.84   -32.96
 695 VAL   ( 113-)  E      CA    -6.3    24.12    33.23
 695 VAL   ( 113-)  E      CB     9.9   -19.96   -32.96
 739 VAL   ( 157-)  E      CA    -7.2    22.82    33.23
 739 VAL   ( 157-)  E      CB    10.0   -19.90   -32.96
 758 PRO   ( 176-)  E      N      8.4    25.02    -2.48
 758 PRO   ( 176-)  E      CA    -7.0    28.26    38.15
 959 VAL   ( 377-)  E      CB     9.0   -21.12   -32.96
1010 VAL   ( 428-)  E      CA    -8.0    21.58    33.23
1010 VAL   ( 428-)  E      CB    11.6   -17.80   -32.96
1317 VAL   ( 145-)  H      CA    -6.9    23.20    33.23
1317 VAL   ( 145-)  H      CB    11.2   -18.30   -32.96
1348 PRO   ( 176-)  H      N      8.2    24.35    -2.48
1348 PRO   ( 176-)  H      CA    -7.6    27.39    38.15
1689 LEU   (  42-)  I      CG     6.0   -22.38   -33.01
1698 VAL   (  51-)  I      CB     8.2   -22.25   -32.96
1919 VAL   ( 157-)  K      CA    -7.6    22.24    33.23
1919 VAL   ( 157-)  K      CB    10.3   -19.51   -32.96
1937 LYS   ( 175-)  K      CA    -6.5    23.19    33.92
1938 PRO   ( 176-)  K      N      7.3    21.55    -2.48
1938 PRO   ( 176-)  K      CA    -7.4    27.77    38.15
2052 LEU   ( 290-)  K      CG     7.1   -20.57   -33.01
2271 VAL   (  42-)  L      CB     9.6   -20.32   -32.96
2405 PRO   ( 176-)  L      N      8.2    24.34    -2.48
2405 PRO   ( 176-)  L      CA    -8.2    26.60    38.15
2418 VAL   ( 189-)  L      CA    -7.6    22.23    33.23
2418 VAL   ( 189-)  L      CB    11.7   -17.66   -32.96
2435 VAL   ( 206-)  L      CB     9.4   -20.68   -32.96
2494 VAL   ( 265-)  L      CB    11.1   -18.46   -32.96
2636 LEU   ( 407-)  L      CG     6.2   -22.05   -33.01
2888 VAL   (  69-)  O      CB     9.8   -20.17   -32.96
2995 PRO   ( 176-)  O      N      7.9    23.57    -2.48
2995 PRO   ( 176-)  O      CA    -8.1    26.80    38.15
3584 LYS   ( 175-)  R      C    -16.2   -24.39     0.11
3585 PRO   ( 176-)  R      N    -17.6   -60.23    -2.48
3671 VAL   ( 262-)  R      CB    10.6   -19.03   -32.96
4037 VAL   (  30-)  T      CA    -7.4    22.51    33.23
4037 VAL   (  30-)  T      CB     9.2   -20.86   -32.96
4164 VAL   (  42-)  V      CB     9.7   -20.29   -32.96
4298 PRO   ( 176-)  V      N      7.2    21.10    -2.48
4298 PRO   ( 176-)  V      CA    -8.0    26.85    38.15
4300 LEU   ( 178-)  V      CG     6.3   -21.87   -33.01
4468 VAL   ( 346-)  V      CA    -8.1    21.42    33.23
4468 VAL   ( 346-)  V      CB    11.8   -17.55   -32.96
The average deviation= 1.430

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.

 468 MET   (   1-)  C    5.09
2634 GLY   ( 405-)  L    4.75
3585 PRO   ( 176-)  R    4.51

Torsion-related checks

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.

1788 THR   (  26-)  K    -3.4
2255 THR   (  26-)  L    -3.3
 608 THR   (  26-)  E    -3.3
3435 THR   (  26-)  R    -3.3
2845 THR   (  26-)  O    -3.3
1198 THR   (  26-)  H    -3.3
4148 THR   (  26-)  V    -3.3
  18 THR   (  26-)  B    -3.2
2405 PRO   ( 176-)  L    -3.1
 168 PRO   ( 176-)  B    -3.1
2995 PRO   ( 176-)  O    -3.1
4298 PRO   ( 176-)  V    -3.1
1348 PRO   ( 176-)  H    -3.1
 758 PRO   ( 176-)  E    -3.1
1938 PRO   ( 176-)  K    -2.9
4016 LEU   (   9-)  T    -2.7
 361 VAL   ( 369-)  B    -2.6
3893 LEU   (   9-)  S    -2.6
2713 LEU   (   9-)  M    -2.6
3188 VAL   ( 369-)  O    -2.6
2598 VAL   ( 369-)  L    -2.6
 476 LEU   (   9-)  C    -2.6
4606 LEU   (   9-)  W    -2.6
1656 LEU   (   9-)  I    -2.6
1066 LEU   (   9-)  F    -2.6
And so on for a total of 106 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.

   2 SER   (  10-)  B  Poor phi/psi
  15 THR   (  23-)  B  omega poor
  17 TYR   (  25-)  B  omega poor
  27 ASP   (  35-)  B  omega poor
  54 SER   (  62-)  B  Poor phi/psi
  57 THR   (  65-)  B  Poor phi/psi
  73 LYS   (  81-)  B  omega poor
  89 TYR   (  97-)  B  omega poor
 111 SER   ( 119-)  B  omega poor
 155 ASN   ( 163-)  B  Poor phi/psi
 163 GLY   ( 171-)  B  omega poor
 164 CYS   ( 172-)  B  Poor phi/psi
 167 LYS   ( 175-)  B  PRO omega poor
 168 PRO   ( 176-)  B  Poor phi/psi
 191 PHE   ( 199-)  B  omega poor
 199 ASN   ( 207-)  B  Poor phi/psi, omega poor
 289 MET   ( 297-)  B  Poor phi/psi
 293 ILE   ( 301-)  B  omega poor
 298 ASN   ( 306-)  B  omega poor
 314 GLY   ( 322-)  B  omega poor
 323 VAL   ( 331-)  B  Poor phi/psi
 361 VAL   ( 369-)  B  Poor phi/psi
 362 SER   ( 370-)  B  Poor phi/psi, omega poor
 390 SER   ( 398-)  B  omega poor
 395 GLY   ( 403-)  B  omega poor
And so on for a total of 349 lines.

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.

 351 SER   ( 359-)  B    0.39
 941 SER   ( 359-)  E    0.39
1531 SER   ( 359-)  H    0.39
2588 SER   ( 359-)  L    0.39
3768 SER   ( 359-)  R    0.39

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 GLU   (  12-)  B      0
   7 ALA   (  15-)  B      0
   9 VAL   (  17-)  B      0
  10 LYS   (  18-)  B      0
  15 THR   (  23-)  B      0
  17 TYR   (  25-)  B      0
  18 THR   (  26-)  B      0
  38 PRO   (  46-)  B      0
  53 SER   (  61-)  B      0
  54 SER   (  62-)  B      0
  55 THR   (  63-)  B      0
  58 TRP   (  66-)  B      0
  62 TRP   (  70-)  B      0
  66 LEU   (  74-)  B      0
  67 THR   (  75-)  B      0
  68 ASN   (  76-)  B      0
  77 TYR   (  85-)  B      0
  80 GLU   (  88-)  B      0
  83 ALA   (  91-)  B      0
  86 GLU   (  94-)  B      0
  87 ASN   (  95-)  B      0
  99 LEU   ( 107-)  B      0
 102 GLU   ( 110-)  B      0
 112 ILE   ( 120-)  B      0
 113 VAL   ( 121-)  B      0
And so on for a total of 1762 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 : 7.742

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!

1509 GLY   ( 337-)  H   2.31   20
2566 GLY   ( 337-)  L   2.23   20
 329 GLY   ( 337-)  B   2.23   20
3156 GLY   ( 337-)  O   2.23   20
4459 GLY   ( 337-)  V   2.23   20
3746 GLY   ( 337-)  R   2.20   21
 919 GLY   ( 337-)  E   2.19   18
2099 GLY   ( 337-)  K   2.14   21

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]

  41 PRO   (  49-)  B    0.10 LOW
 168 PRO   ( 176-)  B    0.46 HIGH
 462 PRO   ( 470-)  B    0.04 LOW
 626 PRO   (  44-)  E    0.19 LOW
 631 PRO   (  49-)  E    0.12 LOW
 632 PRO   (  50-)  E    0.18 LOW
 758 PRO   ( 176-)  E    0.48 HIGH
1052 PRO   ( 470-)  E    0.06 LOW
1216 PRO   (  44-)  H    0.20 LOW
1221 PRO   (  49-)  H    0.10 LOW
1348 PRO   ( 176-)  H    0.45 HIGH
1642 PRO   ( 470-)  H    0.01 LOW
1666 PRO   (  19-)  I    0.18 LOW
1687 PRO   (  40-)  I    0.17 LOW
1811 PRO   (  49-)  K    0.12 LOW
1812 PRO   (  50-)  K    0.16 LOW
1938 PRO   ( 176-)  K    0.47 HIGH
2232 PRO   ( 470-)  K    0.08 LOW
2278 PRO   (  49-)  L    0.14 LOW
2699 PRO   ( 470-)  L    0.05 LOW
2777 PRO   (  73-)  M    0.18 LOW
2868 PRO   (  49-)  O    0.15 LOW
2995 PRO   ( 176-)  O    0.46 HIGH
3289 PRO   ( 470-)  O    0.05 LOW
3334 PRO   (  40-)  P    0.18 LOW
3458 PRO   (  49-)  R    0.12 LOW
3459 PRO   (  50-)  R    0.18 LOW
3585 PRO   ( 176-)  R    0.72 HIGH
3879 PRO   ( 470-)  R    0.01 LOW
3957 PRO   (  73-)  S    0.20 LOW
4080 PRO   (  73-)  T    0.18 LOW
4171 PRO   (  49-)  V    0.12 LOW
4298 PRO   ( 176-)  V    0.47 HIGH
4592 PRO   ( 470-)  V    0.02 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].

  81 PRO   (  89-)  B  -113.1 envelop C-gamma (-108 degrees)
 143 PRO   ( 151-)  B   111.4 envelop C-beta (108 degrees)
 144 PRO   ( 152-)  B   105.3 envelop C-beta (108 degrees)
 168 PRO   ( 176-)  B  -152.8 envelop C-delta (-144 degrees)
 202 PRO   ( 210-)  B   107.1 envelop C-beta (108 degrees)
 402 PRO   ( 410-)  B  -115.7 envelop C-gamma (-108 degrees)
 671 PRO   (  89-)  E  -113.3 envelop C-gamma (-108 degrees)
 733 PRO   ( 151-)  E   106.2 envelop C-beta (108 degrees)
 734 PRO   ( 152-)  E   100.4 envelop C-beta (108 degrees)
 758 PRO   ( 176-)  E  -155.4 half-chair N/C-delta (-162 degrees)
 792 PRO   ( 210-)  E   109.7 envelop C-beta (108 degrees)
1097 PRO   (  40-)  F   -41.7 envelop C-alpha (-36 degrees)
1261 PRO   (  89-)  H  -113.6 envelop C-gamma (-108 degrees)
1323 PRO   ( 151-)  H   115.7 envelop C-beta (108 degrees)
1324 PRO   ( 152-)  H   109.0 envelop C-beta (108 degrees)
1348 PRO   ( 176-)  H  -155.3 half-chair N/C-delta (-162 degrees)
1382 PRO   ( 210-)  H   113.2 envelop C-beta (108 degrees)
1851 PRO   (  89-)  K  -119.0 half-chair C-delta/C-gamma (-126 degrees)
1913 PRO   ( 151-)  K   101.3 envelop C-beta (108 degrees)
1914 PRO   ( 152-)  K   100.9 envelop C-beta (108 degrees)
1938 PRO   ( 176-)  K  -152.6 envelop C-delta (-144 degrees)
1972 PRO   ( 210-)  K   105.7 envelop C-beta (108 degrees)
2172 PRO   ( 410-)  K  -114.1 envelop C-gamma (-108 degrees)
2318 PRO   (  89-)  L  -113.8 envelop C-gamma (-108 degrees)
2380 PRO   ( 151-)  L   109.0 envelop C-beta (108 degrees)
And so on for a total of 54 lines.

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.

2009 CYS   ( 247-)  K      SG   <->  3066 CYS   ( 247-)  O      SG   0.95    2.50  INTRA
 239 CYS   ( 247-)  B      SG   <->  2476 CYS   ( 247-)  L      SG   0.88    2.57  INTRA
 829 CYS   ( 247-)  E      SG   <->  1419 CYS   ( 247-)  H      SG   0.84    2.61  INTRA
3656 CYS   ( 247-)  R      SG   <->  4369 CYS   ( 247-)  V      SG   0.80    2.65  INTRA
2235 ASP   ( 473-)  K      OD2  <->  4751 HOH   (2273 )  K      O    0.69    1.71  INTRA BF
3086 HIS   ( 267-)  O      CD2  <->  3096 ASN   ( 277-)  O      ND2  0.26    2.84  INTRA BL
4420 HIS   ( 298-)  V      ND1  <->  4424 ASP   ( 302-)  V      OD2  0.25    2.45  INTRA BL
 720 LEU   ( 138-)  E      O    <->   898 LYS   ( 316-)  E      NZ   0.24    2.46  INTRA BL
1330 GLU   ( 158-)  H      OE2  <->  1497 HIS   ( 325-)  H      NE2  0.24    2.46  INTRA BL
2496 HIS   ( 267-)  L      CD2  <->  2506 ASN   ( 277-)  L      ND2  0.23    2.87  INTRA BL
4389 HIS   ( 267-)  V      CD2  <->  4399 ASN   ( 277-)  V      ND2  0.23    2.87  INTRA BL
1310 LEU   ( 138-)  H      O    <->  1488 LYS   ( 316-)  H      NZ   0.22    2.48  INTRA BL
 259 HIS   ( 267-)  B      CD2  <->   269 ASN   ( 277-)  B      ND2  0.22    2.88  INTRA BL
2029 HIS   ( 267-)  K      CD2  <->  2039 ASN   ( 277-)  K      ND2  0.21    2.89  INTRA BL
 111 SER   ( 119-)  B      OG   <->  2434 ASN   ( 205-)  L      ND2  0.21    2.49  INTRA BL
 849 HIS   ( 267-)  E      CD2  <->   859 ASN   ( 277-)  E      ND2  0.21    2.89  INTRA BL
2957 LEU   ( 138-)  O      O    <->  3135 LYS   ( 316-)  O      NZ   0.21    2.49  INTRA BL
4363 ASN   ( 241-)  V      ND2  <->  4365 THR   ( 243-)  V      OG1  0.21    2.49  INTRA BL
1967 ASN   ( 205-)  K      ND2  <->  2938 SER   ( 119-)  O      OG   0.20    2.50  INTRA BL
3676 HIS   ( 267-)  R      CD2  <->  3686 ASN   ( 277-)  R      ND2  0.19    2.91  INTRA BL
3206 MET   ( 387-)  O      N    <->  3207 PRO   ( 388-)  O      CD   0.19    2.81  INTRA BL
 150 GLU   ( 158-)  B      OE2  <->   317 HIS   ( 325-)  B      NE2  0.19    2.51  INTRA BL
3547 LEU   ( 138-)  R      O    <->  3725 LYS   ( 316-)  R      NZ   0.19    2.51  INTRA BL
1439 HIS   ( 267-)  H      CD2  <->  1449 ASN   ( 277-)  H      ND2  0.19    2.91  INTRA BL
1068 LYS   (  11-)  F      NZ   <->  4748 HOH   (2018 )  F      O    0.19    2.51  INTRA
And so on for a total of 365 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

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: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

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: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

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.

2950 ARG   ( 131-)  O      -6.51
 713 ARG   ( 131-)  E      -6.50
2360 ARG   ( 131-)  L      -6.48
1893 ARG   ( 131-)  K      -6.47
4253 ARG   ( 131-)  V      -6.46
 123 ARG   ( 131-)  B      -6.45
1303 ARG   ( 131-)  H      -6.29
3540 ARG   ( 131-)  R      -6.28
 731 GLN   ( 149-)  E      -6.24
3558 GLN   ( 149-)  R      -6.22
 141 GLN   ( 149-)  B      -6.22
2968 GLN   ( 149-)  O      -6.20
2378 GLN   ( 149-)  L      -6.19
1321 GLN   ( 149-)  H      -6.17
4271 GLN   ( 149-)  V      -6.08
1911 GLN   ( 149-)  K      -6.07
1021 ARG   ( 439-)  E      -5.74
3848 ARG   ( 439-)  R      -5.74
2668 ARG   ( 439-)  L      -5.73
3258 ARG   ( 439-)  O      -5.73
1611 ARG   ( 439-)  H      -5.72
4561 ARG   ( 439-)  V      -5.71
2201 ARG   ( 439-)  K      -5.71
 431 ARG   ( 439-)  B      -5.71
 596 LYS   (  14-)  E      -5.52
And so on for a total of 76 lines.

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: 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: 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: 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: 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: 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: 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: 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

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.

   4 GLU   (  12-)  B   -3.30
2831 GLU   (  12-)  O   -3.30
1184 GLU   (  12-)  H   -3.29
3893 LEU   (   9-)  S   -3.11
4421 ALA   ( 299-)  V   -2.98
3118 ALA   ( 299-)  O   -2.93
3708 ALA   ( 299-)  R   -2.93
1471 ALA   ( 299-)  H   -2.91
2528 ALA   ( 299-)  L   -2.88
2061 ALA   ( 299-)  K   -2.87
 881 ALA   ( 299-)  E   -2.84
1654 LEU   (   7-)  I   -2.83
 291 ALA   ( 299-)  B   -2.83
 577 VAL   ( 110-)  C   -2.82
2241 GLU   (  12-)  L   -2.81
4134 GLU   (  12-)  V   -2.81
 594 GLU   (  12-)  E   -2.80
3421 GLU   (  12-)  R   -2.77
4707 VAL   ( 110-)  W   -2.69
1167 VAL   ( 110-)  F   -2.68
3994 VAL   ( 110-)  S   -2.68
4117 VAL   ( 110-)  T   -2.67
3404 VAL   ( 110-)  P   -2.66
2814 VAL   ( 110-)  M   -2.65
1757 VAL   ( 110-)  I   -2.60
1774 GLU   (  12-)  K   -2.56

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.

4013 ILE   (   6-)  T     - 4016 LEU   (   9-)  T        -2.12

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

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: H

Note: Second generation quality Z-score plot

Chain identifier: I

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: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: R

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: V

Note: Second generation quality Z-score plot

Chain identifier: W

Water, ion, and hydrogenbond related checks

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.

4751 HOH   (2174 )  K      O
4751 HOH   (2275 )  K      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.

  78 HIS   (  86-)  B
 145 HIS   ( 153-)  B
 148 GLN   ( 156-)  B
 176 ASN   ( 184-)  B
 221 GLN   ( 229-)  B
 230 HIS   ( 238-)  B
 233 ASN   ( 241-)  B
 259 HIS   ( 267-)  B
 269 ASN   ( 277-)  B
 274 HIS   ( 282-)  B
 296 GLN   ( 304-)  B
 412 ASN   ( 420-)  B
 424 ASN   ( 432-)  B
 492 GLN   (  25-)  C
 496 GLN   (  29-)  C
 735 HIS   ( 153-)  E
 738 GLN   ( 156-)  E
 766 ASN   ( 184-)  E
 820 HIS   ( 238-)  E
 823 ASN   ( 241-)  E
 849 HIS   ( 267-)  E
 859 ASN   ( 277-)  E
 864 HIS   ( 282-)  E
 886 GLN   ( 304-)  E
 968 HIS   ( 386-)  E
And so on for a total of 130 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.

  43 GLU   (  51-)  B      N
  57 THR   (  65-)  B      OG1
  59 THR   (  67-)  B      N
  68 ASN   (  76-)  B      N
  75 ARG   (  83-)  B      NE
 159 ARG   ( 167-)  B      N
 167 LYS   ( 175-)  B      N
 169 LYS   ( 177-)  B      NZ
 170 LEU   ( 178-)  B      N
 171 GLY   ( 179-)  B      N
 203 PHE   ( 211-)  B      N
 209 ARG   ( 217-)  B      NH1
 231 TYR   ( 239-)  B      OH
 238 THR   ( 246-)  B      N
 287 ARG   ( 295-)  B      NE
 315 GLY   ( 323-)  B      N
 326 LYS   ( 334-)  B      NZ
 356 PHE   ( 364-)  B      N
 373 GLY   ( 381-)  B      N
 375 HIS   ( 383-)  B      N
 396 GLY   ( 404-)  B      N
 405 ASN   ( 413-)  B      ND2
 469 GLN   (   2-)  C      N
 482 LEU   (  15-)  C      N
 496 GLN   (  29-)  C      NE2
And so on for a total of 250 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.

 260 ASP   ( 268-)  B      OD1
 260 ASP   ( 268-)  B      OD2
 319 HIS   ( 327-)  B      ND1
 378 HIS   ( 386-)  B      NE2
 393 GLN   ( 401-)  B      OE1
 850 ASP   ( 268-)  E      OD1
 850 ASP   ( 268-)  E      OD2
 876 HIS   ( 294-)  E      NE2
 909 HIS   ( 327-)  E      ND1
1440 ASP   ( 268-)  H      OD1
1440 ASP   ( 268-)  H      OD2
1499 HIS   ( 327-)  H      ND1
1573 GLN   ( 401-)  H      OE1
1636 GLU   ( 464-)  H      OE1
2030 ASP   ( 268-)  K      OD1
2030 ASP   ( 268-)  K      OD2
2497 ASP   ( 268-)  L      OD1
2497 ASP   ( 268-)  L      OD2
2521 HIS   ( 292-)  L      NE2
2556 HIS   ( 327-)  L      NE2
3087 ASP   ( 268-)  O      OD1
3087 ASP   ( 268-)  O      OD2
3146 HIS   ( 327-)  O      ND1
3220 GLN   ( 401-)  O      OE1
3677 ASP   ( 268-)  R      OD1
3677 ASP   ( 268-)  R      OD2
3736 HIS   ( 327-)  R      ND1
3810 GLN   ( 401-)  R      OE1
4390 ASP   ( 268-)  V      OD1
4390 ASP   ( 268-)  V      OD2
4449 HIS   ( 327-)  V      ND1
4523 GLN   ( 401-)  V      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

4729  CA   ( 476-)  B     0.42   1.16 Is perhaps  K
4731  CA   ( 476-)  E     0.42   1.16 Is perhaps  K
4733  CA   ( 476-)  H     0.48   1.38 Scores about as good as  K
4735  CA   ( 476-)  K     0.44   1.26 Scores about as good as  K
4737  CA   ( 476-)  L     0.48   1.40 Scores about as good as  K
4739  CA   ( 476-)  O     0.42   1.16 Is perhaps  K
4741  CA   ( 476-)  R     0.47   1.37 Scores about as good as  K
4743  CA   ( 476-)  V     0.47   1.31 Scores about as good as  K

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.

4745 HOH   (2079 )  B      O  0.99  K  4 NCS 7/7
4745 HOH   (2087 )  B      O  0.86  K  4 NCS 6/6
4745 HOH   (2248 )  B      O  1.00  K  4 NCS 5/5
4747 HOH   (2104 )  E      O  1.03  K  4 NCS 7/7
4747 HOH   (2115 )  E      O  0.98  K  4 NCS 7/7
4747 HOH   (2137 )  E      O  1.13  K  4 NCS 7/7
4747 HOH   (2227 )  E      O  0.97  K  6 Ion-B
4747 HOH   (2238 )  E      O  0.94  K  4 NCS 7/7
4747 HOH   (2273 )  E      O  1.13  K  4 NCS 5/5
4749 HOH   (2051 )  H      O  1.04  K  4 NCS 4/4
4749 HOH   (2053 )  H      O  1.12  K  4 NCS 5/5
4749 HOH   (2133 )  H      O  0.95  K  4 NCS 7/7
4751 HOH   (2257 )  K      O  0.95  K  4 NCS 4/4
4752 HOH   (2082 )  L      O  0.90  K  4 NCS 6/6
4752 HOH   (2206 )  L      O  0.97  K  4 Ion-B
4752 HOH   (2217 )  L      O  1.09  K  4 H2O-B NCS 7/7
4754 HOH   (2052 )  O      O  0.80 NA  4 *2 NCS 6/6
4754 HOH   (2073 )  O      O  0.92  K  4 NCS 5/5
4754 HOH   (2139 )  O      O  1.14  K  4 NCS 7/7
4755 HOH   (2019 )  P      O  0.93  K  4 Ion-B NCS 7/7
4756 HOH   (2029 )  R      O  0.86  K  4 Ion-B NCS 3/3
4756 HOH   (2052 )  R      O  0.88  K  4 Ion-B NCS 5/5
4756 HOH   (2104 )  R      O  0.87  K  5 NCS 7/7
4756 HOH   (2120 )  R      O  0.99  K  4 NCS 7/7
4757 HOH   (2002 )  S      O  0.85  K  4 H2O-B NCS 4/4
4759 HOH   (2243 )  V      O  1.04  K  4 Ion-B NCS 3/3

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.

 152 ASP   ( 160-)  B   H-bonding suggests Asn
 260 ASP   ( 268-)  B   H-bonding suggests Asn
 278 ASP   ( 286-)  B   H-bonding suggests Asn
 576 GLU   ( 109-)  C   H-bonding suggests Gln; but Alt-Rotamer
 742 ASP   ( 160-)  E   H-bonding suggests Asn
 850 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1166 GLU   ( 109-)  F   H-bonding suggests Gln; but Alt-Rotamer
1332 ASP   ( 160-)  H   H-bonding suggests Asn
1440 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
1756 GLU   ( 109-)  I   H-bonding suggests Gln; but Alt-Rotamer
1922 ASP   ( 160-)  K   H-bonding suggests Asn
2030 ASP   ( 268-)  K   H-bonding suggests Asn; but Alt-Rotamer
2389 ASP   ( 160-)  L   H-bonding suggests Asn
2497 ASP   ( 268-)  L   H-bonding suggests Asn
2813 GLU   ( 109-)  M   H-bonding suggests Gln; but Alt-Rotamer
2979 ASP   ( 160-)  O   H-bonding suggests Asn
3087 ASP   ( 268-)  O   H-bonding suggests Asn
3325 ASP   (  31-)  P   H-bonding suggests Asn
3403 GLU   ( 109-)  P   H-bonding suggests Gln; but Alt-Rotamer
3569 ASP   ( 160-)  R   H-bonding suggests Asn
3677 ASP   ( 268-)  R   H-bonding suggests Asn; but Alt-Rotamer
3993 GLU   ( 109-)  S   H-bonding suggests Gln; but Alt-Rotamer
4116 GLU   ( 109-)  T   H-bonding suggests Gln; but Alt-Rotamer
4282 ASP   ( 160-)  V   H-bonding suggests Asn; but Alt-Rotamer
4390 ASP   ( 268-)  V   H-bonding suggests Asn; but Alt-Rotamer
4408 ASP   ( 286-)  V   H-bonding suggests Asn; but Alt-Rotamer
4706 GLU   ( 109-)  W   H-bonding suggests Gln; but Alt-Rotamer

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 :  -1.158
  2nd generation packing quality :  -0.740
  Ramachandran plot appearance   :  -1.197
  chi-1/chi-2 rotamer normality  :  -1.469
  Backbone conformation          :  -0.350

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.489 (tight)
  Bond angles                    :   1.226
  Omega angle restraints         :   1.408 (loose)
  Side chain planarity           :   0.579 (tight)
  Improper dihedral distribution :   1.314
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.053

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.489 (tight)
  Bond angles                    :   1.226
  Omega angle restraints         :   1.408 (loose)
  Side chain planarity           :   0.579 (tight)
  Improper dihedral distribution :   1.314
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.053
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.