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 pdb1uw9.ent

Checks that need to be done early-on in validation

Warning: Cell is non-standard

The unit cell in the CRYST1 card of the PDB file contains angles outside the range 60-120 degrees. A conventional cell has angles within these limits.

The CRYST1 cell dimensions

    A    = 126.073  B   = 178.196  C    = 120.463
    Alpha=  90.000  Beta= 120.350  Gamma=  90.000

Space group name: P 1 21 1

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 126.073  B   = 178.196  C    = 120.463
    Alpha=  90.000  Beta= 120.350  Gamma=  90.000

Dimensions of a reduced cell

    A    = 120.463  B   = 122.712  C    = 178.196
    Alpha=  90.000  Beta=  90.000  Gamma=  62.448

Dimensions of the conventional cell

    A    = 120.463  B   = 178.196  C    = 122.712
    Alpha=  90.000  Beta= 117.552  Gamma=  90.000

Transformation to conventional cell

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

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 : 0.080
CA-only RMS fit for the two chains : 0.033

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 H

All-atom RMS fit for the two chains : 0.058
CA-only RMS fit for the two chains : 0.033

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.

4873 CAP   (1477-)  A  -
4880 CAP   (1477-)  B  -
4889 CAP   (1477-)  E  -
4913 CAP   (1476-)  O  -
4915 CAP   (1478-)  H  -
4924 CAP   (1476-)  R  -
4926 CAP   (1478-)  K  -
4942 CAP   (1476-)  V  -

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.

 704 CYS   ( 247-)  B  -

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.

 704 CYS   ( 247-)  B  -

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: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: R

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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 389 CYS   ( 399-)  A
 547 VAL   (  90-)  B

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 704 CYS   ( 247-)  B    0.75

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) :100.000

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: 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: J

Note: B-factor plot

Chain identifier: K

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: 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.

 177 ARG   ( 187-)  A
 644 ARG   ( 187-)  B
1249 ARG   ( 187-)  E
1858 ARG   ( 187-)  H
2607 ARG   ( 187-)  K
3216 ARG   ( 187-)  O
3821 ARG   ( 187-)  R
4427 ARG   ( 187-)  V

Warning: Tyrosine convention problem

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

  93 TYR   ( 103-)  A
 560 TYR   ( 103-)  B
 983 TYR   (  51-)  C
 999 TYR   (  67-)  C
1036 TYR   ( 104-)  C
1165 TYR   ( 103-)  E
1345 TYR   ( 283-)  E
1588 TYR   (  51-)  F
1604 TYR   (  67-)  F
1774 TYR   ( 103-)  H
2197 TYR   (  51-)  I
2213 TYR   (  67-)  I
2337 TYR   (  51-)  J
2353 TYR   (  67-)  J
2523 TYR   ( 103-)  K
2946 TYR   (  51-)  M
2962 TYR   (  67-)  M
3129 TYR   ( 100-)  O
3312 TYR   ( 283-)  O
3555 TYR   (  51-)  P
3571 TYR   (  67-)  P
3734 TYR   ( 100-)  R
3737 TYR   ( 103-)  R
4160 TYR   (  51-)  T
4176 TYR   (  67-)  T
4340 TYR   ( 100-)  V
4343 TYR   ( 103-)  V
4766 TYR   (  51-)  W
4782 TYR   (  67-)  W

Warning: Phenylalanine convention problem

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

 280 PHE   ( 290-)  A
 392 PHE   ( 402-)  A
 457 PHE   ( 467-)  A
 747 PHE   ( 290-)  B
 859 PHE   ( 402-)  B
 944 PHE   (  12-)  C
 947 PHE   (  15-)  C
 976 PHE   (  44-)  C
 992 PHE   (  60-)  C
1032 PHE   ( 100-)  C
1352 PHE   ( 290-)  E
1464 PHE   ( 402-)  E
1529 PHE   ( 467-)  E
1549 PHE   (  12-)  F
1552 PHE   (  15-)  F
1581 PHE   (  44-)  F
1597 PHE   (  60-)  F
1637 PHE   ( 100-)  F
1961 PHE   ( 290-)  H
2073 PHE   ( 402-)  H
2138 PHE   ( 467-)  H
2158 PHE   (  12-)  I
2161 PHE   (  15-)  I
2190 PHE   (  44-)  I
2206 PHE   (  60-)  I
And so on for a total of 59 lines.

Warning: Aspartic acid convention problem

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

1063 ASP   ( 131-)  C
1668 ASP   ( 131-)  F
2277 ASP   ( 131-)  I
2417 ASP   ( 131-)  J
2453 ASP   (  33-)  K
3026 ASP   ( 131-)  M
3635 ASP   ( 131-)  P
4240 ASP   ( 131-)  T
4846 ASP   ( 131-)  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.

  78 GLU   (  88-)  A
 450 GLU   ( 460-)  A
 545 GLU   (  88-)  B
 917 GLU   ( 460-)  B
 978 GLU   (  46-)  C
 987 GLU   (  55-)  C
1150 GLU   (  88-)  E
1522 GLU   ( 460-)  E
1583 GLU   (  46-)  F
1592 GLU   (  55-)  F
1759 GLU   (  88-)  H
2131 GLU   ( 460-)  H
2192 GLU   (  46-)  I
2201 GLU   (  55-)  I
2332 GLU   (  46-)  J
2341 GLU   (  55-)  J
2508 GLU   (  88-)  K
2880 GLU   ( 460-)  K
2941 GLU   (  46-)  M
2950 GLU   (  55-)  M
3117 GLU   (  88-)  O
3489 GLU   ( 460-)  O
3550 GLU   (  46-)  P
3559 GLU   (  55-)  P
3722 GLU   (  88-)  R
4094 GLU   ( 460-)  R
4155 GLU   (  46-)  T
4164 GLU   (  55-)  T
4328 GLU   (  88-)  V
4700 GLU   ( 460-)  V
4761 GLU   (  46-)  W
4770 GLU   (  55-)  W

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.

 191 KCX   ( 201-)  A      CH     CX
 191 KCX   ( 201-)  A      OX1    OQ1
 191 KCX   ( 201-)  A      OX2    OQ2
 658 KCX   ( 201-)  B      CH     CX
 658 KCX   ( 201-)  B      OX1    OQ1
 658 KCX   ( 201-)  B      OX2    OQ2
1263 KCX   ( 201-)  E      CH     CX
1263 KCX   ( 201-)  E      OX1    OQ1
1263 KCX   ( 201-)  E      OX2    OQ2
1872 KCX   ( 201-)  H      CH     CX
1872 KCX   ( 201-)  H      OX1    OQ1
1872 KCX   ( 201-)  H      OX2    OQ2
2621 KCX   ( 201-)  K      CH     CX
2621 KCX   ( 201-)  K      OX1    OQ1
2621 KCX   ( 201-)  K      OX2    OQ2
3230 KCX   ( 201-)  O      CH     CX
3230 KCX   ( 201-)  O      OX1    OQ1
3230 KCX   ( 201-)  O      OX2    OQ2
3835 KCX   ( 201-)  R      CH     CX
3835 KCX   ( 201-)  R      OX1    OQ1
3835 KCX   ( 201-)  R      OX2    OQ2
4441 KCX   ( 201-)  V      CH     CX
4441 KCX   ( 201-)  V      OX1    OQ1
4441 KCX   ( 201-)  V      OX2    OQ2

Geometric checks

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

 |  0.996852 -0.000002  0.000057|
 | -0.000002  0.996775  0.000033|
 |  0.000057  0.000033  0.996837|
Proposed new scale matrix

 |  0.007957  0.000000  0.004658|
 |  0.000000  0.005630  0.000000|
 |  0.000000  0.000000  0.009651|
With corresponding cell

    A    = 125.680  B   = 177.615  C    = 120.074
    Alpha=  90.001  Beta= 120.347  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 126.073  B   = 178.196  C    = 120.463
    Alpha=  90.000  Beta= 120.350  Gamma=  90.000

Variance: 1636.366
(Under-)estimated Z-score: 29.813

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.

 755 HIS   ( 298-)  B      CG   ND1  CE1 109.61    4.0
 782 HIS   ( 325-)  B      CG   ND1  CE1 109.68    4.1
 817 ARG   ( 360-)  B      CG   CD   NE  103.58   -4.1
 817 ARG   ( 360-)  B      CD   NE   CZ  134.45    7.1
 940 ASN   (   8-)  C     -C    N    CA  130.52    4.9
 940 ASN   (   8-)  C      N    CA   C    92.95   -6.5
1545 ASN   (   8-)  F     -C    N    CA  130.61    5.0
1545 ASN   (   8-)  F      N    CA   C    92.06   -6.8
1996 HIS   ( 325-)  H      CG   ND1  CE1 109.62    4.0
2154 ASN   (   8-)  I     -C    N    CA  129.74    4.5
2154 ASN   (   8-)  I      N    CA   C    93.10   -6.5
2294 ASN   (   8-)  J     -C    N    CA  130.07    4.7
2294 ASN   (   8-)  J      N    CA   C    93.25   -6.4
2745 HIS   ( 325-)  K      CG   ND1  CE1 109.65    4.1
2903 ASN   (   8-)  M     -C    N    CA  129.88    4.5
2903 ASN   (   8-)  M      N    CA   C    93.89   -6.2
3512 ASN   (   8-)  P     -C    N    CA  129.28    4.2
3512 ASN   (   8-)  P      N    CA   C    93.88   -6.2
4020 HIS   ( 386-)  R      CG   ND1  CE1 109.64    4.0
4117 ASN   (   8-)  T     -C    N    CA  129.49    4.3
4117 ASN   (   8-)  T      N    CA   C    94.24   -6.1
4723 ASN   (   8-)  W     -C    N    CA  130.15    4.7
4723 ASN   (   8-)  W      N    CA   C    92.88   -6.5

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.

  78 GLU   (  88-)  A
 177 ARG   ( 187-)  A
 450 GLU   ( 460-)  A
 545 GLU   (  88-)  B
 644 ARG   ( 187-)  B
 917 GLU   ( 460-)  B
 978 GLU   (  46-)  C
 987 GLU   (  55-)  C
1063 ASP   ( 131-)  C
1150 GLU   (  88-)  E
1249 ARG   ( 187-)  E
1522 GLU   ( 460-)  E
1583 GLU   (  46-)  F
1592 GLU   (  55-)  F
1668 ASP   ( 131-)  F
1759 GLU   (  88-)  H
1858 ARG   ( 187-)  H
2131 GLU   ( 460-)  H
2192 GLU   (  46-)  I
2201 GLU   (  55-)  I
2277 ASP   ( 131-)  I
2332 GLU   (  46-)  J
2341 GLU   (  55-)  J
2417 ASP   ( 131-)  J
2453 ASP   (  33-)  K
2508 GLU   (  88-)  K
2607 ARG   ( 187-)  K
2880 GLU   ( 460-)  K
2941 GLU   (  46-)  M
2950 GLU   (  55-)  M
3026 ASP   ( 131-)  M
3117 GLU   (  88-)  O
3216 ARG   ( 187-)  O
3489 GLU   ( 460-)  O
3550 GLU   (  46-)  P
3559 GLU   (  55-)  P
3635 ASP   ( 131-)  P
3722 GLU   (  88-)  R
3821 ARG   ( 187-)  R
4094 GLU   ( 460-)  R
4155 GLU   (  46-)  T
4164 GLU   (  55-)  T
4240 ASP   ( 131-)  T
4328 GLU   (  88-)  V
4427 ARG   ( 187-)  V
4700 GLU   ( 460-)  V
4761 GLU   (  46-)  W
4770 GLU   (  55-)  W
4846 ASP   ( 131-)  W

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.

1545 ASN   (   8-)  F    6.44
4723 ASN   (   8-)  W    6.17
 940 ASN   (   8-)  C    6.14
2154 ASN   (   8-)  I    6.09
2294 ASN   (   8-)  J    6.05
3512 ASN   (   8-)  P    5.84
2903 ASN   (   8-)  M    5.84
4117 ASN   (   8-)  T    5.72

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.

3634 ARG   ( 130-)  P    -2.5
1062 ARG   ( 130-)  C    -2.5
2416 ARG   ( 130-)  J    -2.5
1667 ARG   ( 130-)  F    -2.5
4845 ARG   ( 130-)  W    -2.5
4239 ARG   ( 130-)  T    -2.5
3025 ARG   ( 130-)  M    -2.5
2276 ARG   ( 130-)  I    -2.5
1050 ILE   ( 118-)  C    -2.3
3622 ILE   ( 118-)  P    -2.3
2264 ILE   ( 118-)  I    -2.3
2404 ILE   ( 118-)  J    -2.3
3013 ILE   ( 118-)  M    -2.3
4833 ILE   ( 118-)  W    -2.3
4227 ILE   ( 118-)  T    -2.3
 120 LEU   ( 130-)  A    -2.3
1655 ILE   ( 118-)  F    -2.3
4370 LEU   ( 130-)  V    -2.3
 944 PHE   (  12-)  C    -2.3
2298 PHE   (  12-)  J    -2.3
2158 PHE   (  12-)  I    -2.3
3873 TYR   ( 239-)  R    -2.2
4727 PHE   (  12-)  W    -2.2
 229 TYR   ( 239-)  A    -2.2
2907 PHE   (  12-)  M    -2.2
And so on for a total of 80 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.

  13 THR   (  23-)  A  omega poor
  31 ARG   (  41-)  A  omega poor
  52 SER   (  62-)  A  Poor phi/psi
  55 THR   (  65-)  A  omega poor
  87 TYR   (  97-)  A  omega poor
 153 ASN   ( 163-)  A  Poor phi/psi
 162 CYS   ( 172-)  A  Poor phi/psi
 165 LYS   ( 175-)  A  PRO omega poor
 189 PHE   ( 199-)  A  omega poor
 197 ASN   ( 207-)  A  Poor phi/psi
 253 PRO   ( 263-)  A  omega poor
 287 MET   ( 297-)  A  Poor phi/psi
 291 ILE   ( 301-)  A  omega poor
 321 VAL   ( 331-)  A  Poor phi/psi
 340 ARG   ( 350-)  A  omega poor
 360 SER   ( 370-)  A  Poor phi/psi
 498 ARG   (  41-)  B  omega poor
 519 SER   (  62-)  B  Poor phi/psi
 522 THR   (  65-)  B  omega poor
 620 ASN   ( 163-)  B  Poor phi/psi
 629 CYS   ( 172-)  B  Poor phi/psi
 632 LYS   ( 175-)  B  PRO omega poor
 656 PHE   ( 199-)  B  omega poor
 664 ASN   ( 207-)  B  Poor phi/psi
 720 PRO   ( 263-)  B  omega poor
And so on for a total of 195 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.

1509 SER   ( 447-)  E    0.35
 269 SER   ( 279-)  A    0.36
2699 SER   ( 279-)  K    0.36
3308 SER   ( 279-)  O    0.36
 736 SER   ( 279-)  B    0.36
1341 SER   ( 279-)  E    0.36
3913 SER   ( 279-)  R    0.36
4519 SER   ( 279-)  V    0.36
4081 SER   ( 447-)  R    0.37
1950 SER   ( 279-)  H    0.37

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!

   5 ALA   (  15-)  A      0
  13 THR   (  23-)  A      0
  14 TYR   (  24-)  A      0
  15 TYR   (  25-)  A      0
  16 THR   (  26-)  A      0
  36 PRO   (  46-)  A      0
  51 SER   (  61-)  A      0
  52 SER   (  62-)  A      0
  53 THR   (  63-)  A      0
  56 TRP   (  66-)  A      0
  60 TRP   (  70-)  A      0
  64 LEU   (  74-)  A      0
  73 ARG   (  83-)  A      0
  75 TYR   (  85-)  A      0
  76 ASP   (  86-)  A      0
  81 PRO   (  91-)  A      0
  84 ASP   (  94-)  A      0
  85 ASN   (  95-)  A      0
  86 GLN   (  96-)  A      0
  94 HYP   ( 104-)  A      0
 100 GLU   ( 110-)  A      0
 113 ASN   ( 123-)  A      0
 114 VAL   ( 124-)  A      0
 117 PHE   ( 127-)  A      0
 127 ASP   ( 137-)  A      0
And so on for a total of 1895 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

3971 GLY   ( 337-)  R   2.39   10
4577 GLY   ( 337-)  V   2.36   10
2825 GLY   ( 405-)  K   1.65   80
4645 GLY   ( 405-)  V   1.63   80
2076 GLY   ( 405-)  H   1.62   80
 395 GLY   ( 405-)  A   1.61   80
1467 GLY   ( 405-)  E   1.59   80
3434 GLY   ( 405-)  O   1.58   80
 862 GLY   ( 405-)  B   1.58   80
4039 GLY   ( 405-)  R   1.57   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  94 HYP   ( 104-)  A    0.07 LOW
 141 HYP   ( 151-)  A    0.08 LOW
 561 HYP   ( 104-)  B    0.06 LOW
 608 HYP   ( 151-)  B    0.08 LOW
 720 PRO   ( 263-)  B    0.18 LOW
1166 HYP   ( 104-)  E    0.06 LOW
1213 HYP   ( 151-)  E    0.08 LOW
1775 HYP   ( 104-)  H    0.06 LOW
1822 HYP   ( 151-)  H    0.08 LOW
1934 PRO   ( 263-)  H    0.18 LOW
2524 HYP   ( 104-)  K    0.06 LOW
2571 HYP   ( 151-)  K    0.09 LOW
2683 PRO   ( 263-)  K    0.18 LOW
3133 HYP   ( 104-)  O    0.06 LOW
3180 HYP   ( 151-)  O    0.08 LOW
3292 PRO   ( 263-)  O    0.15 LOW
3738 HYP   ( 104-)  R    0.07 LOW
3785 HYP   ( 151-)  R    0.09 LOW
4290 PRO   (  50-)  V    0.19 LOW
4344 HYP   ( 104-)  V    0.06 LOW
4391 HYP   ( 151-)  V    0.08 LOW
4503 PRO   ( 263-)  V    0.18 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].

  36 PRO   (  46-)  A  -127.2 half-chair C-delta/C-gamma (-126 degrees)
  40 PRO   (  50-)  A  -115.3 envelop C-gamma (-108 degrees)
 503 PRO   (  46-)  B  -133.5 half-chair C-delta/C-gamma (-126 degrees)
 507 PRO   (  50-)  B  -115.9 envelop C-gamma (-108 degrees)
 972 PRO   (  40-)  C    48.7 half-chair C-delta/C-gamma (54 degrees)
1058 PRO   ( 126-)  C  -118.8 half-chair C-delta/C-gamma (-126 degrees)
1108 PRO   (  46-)  E  -128.0 half-chair C-delta/C-gamma (-126 degrees)
1112 PRO   (  50-)  E  -113.7 envelop C-gamma (-108 degrees)
1543 PRO   (   6-)  F   -63.5 envelop C-beta (-72 degrees)
1577 PRO   (  40-)  F    45.8 half-chair C-delta/C-gamma (54 degrees)
1663 PRO   ( 126-)  F  -119.3 half-chair C-delta/C-gamma (-126 degrees)
1717 PRO   (  46-)  H  -128.7 half-chair C-delta/C-gamma (-126 degrees)
2186 PRO   (  40-)  I    45.9 half-chair C-delta/C-gamma (54 degrees)
2272 PRO   ( 126-)  I  -118.4 half-chair C-delta/C-gamma (-126 degrees)
2292 PRO   (   6-)  J   -61.8 half-chair C-beta/C-alpha (-54 degrees)
2326 PRO   (  40-)  J    49.5 half-chair C-delta/C-gamma (54 degrees)
2412 PRO   ( 126-)  J  -118.0 half-chair C-delta/C-gamma (-126 degrees)
2466 PRO   (  46-)  K  -129.6 half-chair C-delta/C-gamma (-126 degrees)
2470 PRO   (  50-)  K  -114.8 envelop C-gamma (-108 degrees)
3021 PRO   ( 126-)  M  -119.5 half-chair C-delta/C-gamma (-126 degrees)
3075 PRO   (  46-)  O  -124.9 half-chair C-delta/C-gamma (-126 degrees)
3079 PRO   (  50-)  O  -113.3 envelop C-gamma (-108 degrees)
3510 PRO   (   6-)  P   -65.3 envelop C-beta (-72 degrees)
3544 PRO   (  40-)  P    42.7 envelop C-delta (36 degrees)
3630 PRO   ( 126-)  P  -115.9 envelop C-gamma (-108 degrees)
3680 PRO   (  46-)  R  -130.4 half-chair C-delta/C-gamma (-126 degrees)
3684 PRO   (  50-)  R  -115.6 envelop C-gamma (-108 degrees)
4149 PRO   (  40-)  T    48.6 half-chair C-delta/C-gamma (54 degrees)
4235 PRO   ( 126-)  T  -116.2 envelop C-gamma (-108 degrees)
4286 PRO   (  46-)  V  -126.0 half-chair C-delta/C-gamma (-126 degrees)
4721 PRO   (   6-)  W   -65.0 envelop C-beta (-72 degrees)
4755 PRO   (  40-)  W    46.8 half-chair C-delta/C-gamma (54 degrees)
4841 PRO   ( 126-)  W  -118.0 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

1062 ARG   ( 130-)  C      NH1  <->  4945 HOH   (2073 )  C      O    0.91    1.79  INTRA BF
1545 ASN   (   8-)  F      CG   <->  4947 HOH   (2005 )  F      O    0.69    2.11  INTRA
4239 ARG   ( 130-)  T      NH1  <->  4956 HOH   (2071 )  T      O    0.63    2.07  INTRA BF
 478 ARG   (  21-)  B      NH1  <->  4944 HOH   (2016 )  B      O    0.60    2.10  INTRA
1533 THR   ( 471-)  E      OG1  <->  4946 HOH   (2272 )  E      O    0.48    1.92  INTRA BL
4711 THR   ( 471-)  V      OG1  <->  4957 HOH   (2273 )  V      O    0.45    1.95  INTRA BL
1621 ARG   (  84-)  F      NH1  <->  4947 HOH   (2060 )  F      O    0.42    2.28  INTRA
   1 ALA   (  11-)  A      N    <->  4943 HOH   (2002 )  A      O    0.41    2.29  INTRA BF
2979 ARG   (  84-)  M      NH1  <->  4250 GLY   (  10-)  V      CA   0.38    2.72  INTRA BF
3901 HIS   ( 267-)  R      CD2  <->  3911 ASN   ( 277-)  R      ND2  0.36    2.74  INTRA BL
1621 ARG   (  84-)  F      NH2  <->  4947 HOH   (2059 )  F      O    0.36    2.34  INTRA BF
 257 HIS   ( 267-)  A      CD2  <->   267 ASN   ( 277-)  A      ND2  0.35    2.75  INTRA BL
2979 ARG   (  84-)  M      NH1  <->  4250 GLY   (  10-)  V      N    0.35    2.50  INTRA BF
1329 HIS   ( 267-)  E      CD2  <->  1339 ASN   ( 277-)  E      ND2  0.32    2.78  INTRA BL
4507 HIS   ( 267-)  V      CD2  <->  4517 ASN   ( 277-)  V      ND2  0.31    2.79  INTRA BL
4881 EDO   (1483-)  A      C2   <->  4943 HOH   (2283 )  A      O    0.30    2.50  INTRA
1938 HIS   ( 267-)  H      CD2  <->  1948 ASN   ( 277-)  H      ND2  0.30    2.80  INTRA BL
4896 EDO   (1482-)  E      C2   <->  4946 HOH   (2284 )  E      O    0.30    2.50  INTRA
3050 ARG   (  21-)  O      NH2  <->  4953 HOH   (2014 )  O      O    0.29    2.41  INTRA
1545 ASN   (   8-)  F      ND2  <->  4947 HOH   (2005 )  F      O    0.29    2.41  INTRA
3296 HIS   ( 267-)  O      CD2  <->  3306 ASN   ( 277-)  O      ND2  0.29    2.81  INTRA BL
2687 HIS   ( 267-)  K      CD2  <->  2697 ASN   ( 277-)  K      ND2  0.29    2.81  INTRA BL
1969 HIS   ( 298-)  H      ND1  <->  1973 ASP   ( 302-)  H      OD2  0.28    2.42  INTRA BL
1220 GLU   ( 158-)  E      OE2  <->  1387 HIS   ( 325-)  E      NE2  0.28    2.42  INTRA BL
 724 HIS   ( 267-)  B      CD2  <->   734 ASN   ( 277-)  B      ND2  0.28    2.82  INTRA BL
And so on for a total of 349 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: 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: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

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: 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.

1621 ARG   (  84-)  F      -7.31
2979 ARG   (  84-)  M      -7.29
2230 ARG   (  84-)  I      -7.10
4799 ARG   (  84-)  W      -7.00
4193 ARG   (  84-)  T      -6.58
3037 LYS   (   8-)  O      -6.05
1679 LYS   (   8-)  H      -6.04
2428 LYS   (   8-)  K      -5.99
1016 ARG   (  84-)  C      -5.93
3588 ARG   (  84-)  P      -5.88
2859 ARG   ( 439-)  K      -5.78
4073 ARG   ( 439-)  R      -5.78
1501 ARG   ( 439-)  E      -5.78
 896 ARG   ( 439-)  B      -5.77
4679 ARG   ( 439-)  V      -5.77
2110 ARG   ( 439-)  H      -5.76
3468 ARG   ( 439-)  O      -5.76
 429 ARG   ( 439-)  A      -5.76
2370 ARG   (  84-)  J      -5.71
3043 LYS   (  14-)  O      -5.51
 464 LYS   ( 474-)  A      -5.50
2434 LYS   (  14-)  K      -5.50
4714 LYS   ( 474-)  V      -5.50
1076 LYS   (  14-)  E      -5.50
 471 LYS   (  14-)  B      -5.49
And so on for a total of 98 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: 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: 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: J

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: K

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: 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: 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.

1970 ALA   ( 299-)  H   -2.84
2719 ALA   ( 299-)  K   -2.84
3933 ALA   ( 299-)  R   -2.83
3328 ALA   ( 299-)  O   -2.80
1653 VAL   ( 116-)  F   -2.79
3620 VAL   ( 116-)  P   -2.79
3011 VAL   ( 116-)  M   -2.79
4539 ALA   ( 299-)  V   -2.79
4831 VAL   ( 116-)  W   -2.78
1361 ALA   ( 299-)  E   -2.78
2262 VAL   ( 116-)  I   -2.78
 756 ALA   ( 299-)  B   -2.78
 289 ALA   ( 299-)  A   -2.78
1048 VAL   ( 116-)  C   -2.77
4225 VAL   ( 116-)  T   -2.76
2108 LEU   ( 437-)  H   -2.76
4071 LEU   ( 437-)  R   -2.73
1499 LEU   ( 437-)  E   -2.73
 894 LEU   ( 437-)  B   -2.72
3466 LEU   ( 437-)  O   -2.71
2857 LEU   ( 437-)  K   -2.69
4677 LEU   ( 437-)  V   -2.69
 427 LEU   ( 437-)  A   -2.67
3741 LEU   ( 107-)  R   -2.58
1778 LEU   ( 107-)  H   -2.57
 993 GLY   (  61-)  C   -2.57
1169 LEU   ( 107-)  E   -2.57
4347 LEU   ( 107-)  V   -2.57
2527 LEU   ( 107-)  K   -2.56
  97 LEU   ( 107-)  A   -2.55
3136 LEU   ( 107-)  O   -2.55
 564 LEU   ( 107-)  B   -2.52

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: 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: J

Note: Second generation quality Z-score plot

Chain identifier: K

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: 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

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.

4950 HOH   (2029 )  J      O     55.24  136.96  -26.76

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.

4943 HOH   (2244 )  A      O
4945 HOH   (2055 )  C      O
4951 HOH   (2194 )  K      O
4955 HOH   (2195 )  R      O
4956 HOH   (2007 )  T      O
4956 HOH   (2054 )  T      O
4957 HOH   (2270 )  V      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.

 143 HIS   ( 153-)  A
 146 GLN   ( 156-)  A
 153 ASN   ( 163-)  A
 219 GLN   ( 229-)  A
 228 HIS   ( 238-)  A
 231 ASN   ( 241-)  A
 257 HIS   ( 267-)  A
 267 ASN   ( 277-)  A
 294 GLN   ( 304-)  A
 317 HIS   ( 327-)  A
 376 HIS   ( 386-)  A
 391 GLN   ( 401-)  A
 410 ASN   ( 420-)  A
 422 ASN   ( 432-)  A
 610 HIS   ( 153-)  B
 613 GLN   ( 156-)  B
 620 ASN   ( 163-)  B
 695 HIS   ( 238-)  B
 698 ASN   ( 241-)  B
 724 HIS   ( 267-)  B
 734 ASN   ( 277-)  B
 761 GLN   ( 304-)  B
 784 HIS   ( 327-)  B
 858 GLN   ( 401-)  B
 877 ASN   ( 420-)  B
And so on for a total of 139 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.

  55 THR   (  65-)  A      OG1
  57 THR   (  67-)  A      N
 108 THR   ( 118-)  A      OG1
 157 ARG   ( 167-)  A      N
 157 ARG   ( 167-)  A      NE
 163 THR   ( 173-)  A      OG1
 165 LYS   ( 175-)  A      N
 165 LYS   ( 175-)  A      NZ
 168 LEU   ( 178-)  A      N
 169 GLY   ( 179-)  A      N
 197 ASN   ( 207-)  A      ND2
 201 PHE   ( 211-)  A      N
 207 ARG   ( 217-)  A      NH1
 236 THR   ( 246-)  A      N
 275 ARG   ( 285-)  A      NH1
 285 ARG   ( 295-)  A      NE
 285 ARG   ( 295-)  A      NH1
 293 ARG   ( 303-)  A      NE
 297 HIS   ( 307-)  A      N
 356 GLN   ( 366-)  A      NE2
 369 SER   ( 379-)  A      N
 369 SER   ( 379-)  A      OG
 371 GLY   ( 381-)  A      N
 391 GLN   ( 401-)  A      NE2
 394 GLY   ( 404-)  A      N
And so on for a total of 259 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.

 258 ASP   ( 268-)  A      OD1
 258 ASP   ( 268-)  A      OD2
 282 HIS   ( 292-)  A      NE2
 725 ASP   ( 268-)  B      OD1
 749 HIS   ( 292-)  B      NE2
 843 HIS   ( 386-)  B      NE2
1330 ASP   ( 268-)  E      OD1
1330 ASP   ( 268-)  E      OD2
1354 HIS   ( 292-)  E      NE2
1448 HIS   ( 386-)  E      NE2
1939 ASP   ( 268-)  H      OD1
1963 HIS   ( 292-)  H      NE2
2688 ASP   ( 268-)  K      OD1
2688 ASP   ( 268-)  K      OD2
2747 HIS   ( 327-)  K      ND1
3297 ASP   ( 268-)  O      OD1
3297 ASP   ( 268-)  O      OD2
3321 HIS   ( 292-)  O      NE2
3430 GLN   ( 401-)  O      OE1
3902 ASP   ( 268-)  R      OD1
3961 HIS   ( 327-)  R      ND1
4035 GLN   ( 401-)  R      OE1
4094 GLU   ( 460-)  R      OE1
4508 ASP   ( 268-)  V      OD1
4508 ASP   ( 268-)  V      OD2
4532 HIS   ( 292-)  V      NE2
4626 HIS   ( 386-)  V      NE2

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.

4943 HOH   (2132 )  A      O  0.92  K  4 NCS 7/7
4943 HOH   (2164 )  A      O  1.03  K  4 NCS 7/7
4944 HOH   (2226 )  B      O  0.88  K  4 NCS 6/6
4944 HOH   (2276 )  B      O  0.99  K  4 NCS 7/7
4945 HOH   (2026 )  C      O  0.94  K  4 NCS 6/6
4946 HOH   (2110 )  E      O  1.13  K  4 NCS 7/7
4946 HOH   (2118 )  E      O  0.86  K  4 Ion-B NCS 7/7
4946 HOH   (2137 )  E      O  0.92  K  4 NCS 7/7
4946 HOH   (2155 )  E      O  0.89  K  4 NCS 7/7
4946 HOH   (2212 )  E      O  0.97  K  4 Ion-B NCS 1/1
4946 HOH   (2230 )  E      O  0.86  K  4 NCS 2/2
4947 HOH   (2028 )  F      O  0.87  K  4 NCS 6/6
4947 HOH   (2077 )  F      O  1.11  K  4 NCS 7/7
4947 HOH   (2081 )  F      O  1.04  K  4 ION-B NCS 6/6
4948 HOH   (2173 )  H      O  0.89  K  4 NCS 7/7
4948 HOH   (2224 )  H      O  0.90  K  4 Ion-B NCS 6/6
4948 HOH   (2270 )  H      O  1.05  K  4 NCS 7/7
4950 HOH   (2019 )  J      O  1.07  K  4 NCS 6/6
4950 HOH   (2038 )  J      O  1.03  K  4 NCS 7/7
4951 HOH   (2096 )  K      O  1.09  K  4 NCS 7/7
4953 HOH   (2075 )  O      O  0.89  K  4 NCS 7/7
4953 HOH   (2166 )  O      O  0.92  K  4 Ion-B NCS 7/7
4954 HOH   (2019 )  P      O  0.99  K  4 NCS 6/6
4955 HOH   (2142 )  R      O  0.91  K  4 NCS 7/7
4955 HOH   (2163 )  R      O  0.91  K  4 NCS 7/7
4956 HOH   (2023 )  T      O  1.09  K  4 NCS 6/6
4957 HOH   (2175 )  V      O  0.93  K  4 NCS 7/7
4957 HOH   (2198 )  V      O  0.88  K  4 NCS 7/7
4958 HOH   (2024 )  W      O  1.02  K  4 Ion-B NCS 2/2
4958 HOH   (2047 )  W      O  0.97  K  4 NCS 7/7

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.

  62 ASP   (  72-)  A   H-bonding suggests Asn; Ligand-contact
 150 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 258 ASP   ( 268-)  A   H-bonding suggests Asn
 292 ASP   ( 302-)  A   H-bonding suggests Asn
 529 ASP   (  72-)  B   H-bonding suggests Asn; Ligand-contact
 617 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 725 ASP   ( 268-)  B   H-bonding suggests Asn
1134 ASP   (  72-)  E   H-bonding suggests Asn; Ligand-contact
1330 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1743 ASP   (  72-)  H   H-bonding suggests Asn; Ligand-contact
1939 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
1973 ASP   ( 302-)  H   H-bonding suggests Asn
2492 ASP   (  72-)  K   H-bonding suggests Asn; Ligand-contact
2688 ASP   ( 268-)  K   H-bonding suggests Asn; but Alt-Rotamer
2722 ASP   ( 302-)  K   H-bonding suggests Asn
3101 ASP   (  72-)  O   H-bonding suggests Asn; Ligand-contact
3297 ASP   ( 268-)  O   H-bonding suggests Asn
3706 ASP   (  72-)  R   H-bonding suggests Asn; Ligand-contact
3902 ASP   ( 268-)  R   H-bonding suggests Asn
3936 ASP   ( 302-)  R   H-bonding suggests Asn
4312 ASP   (  72-)  V   H-bonding suggests Asn; Ligand-contact
4400 ASP   ( 160-)  V   H-bonding suggests Asn; but Alt-Rotamer
4508 ASP   ( 268-)  V   H-bonding suggests Asn
4542 ASP   ( 302-)  V   H-bonding suggests Asn

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 :  -0.635
  2nd generation packing quality :  -0.156
  Ramachandran plot appearance   :  -0.445
  chi-1/chi-2 rotamer normality  :  -1.185
  Backbone conformation          :  -0.573

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.435 (tight)
  Bond angles                    :   0.661 (tight)
  Omega angle restraints         :   1.073
  Side chain planarity           :   0.418 (tight)
  Improper dihedral distribution :   0.673
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.049

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.435 (tight)
  Bond angles                    :   0.661 (tight)
  Omega angle restraints         :   1.073
  Side chain planarity           :   0.418 (tight)
  Improper dihedral distribution :   0.673
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.049
==============

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

Bond lengths and angles, protein residues
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Bond lengths and angles, DNA/RNA
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    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
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      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,
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    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.