WHAT IF Check report

This file was created 2012-01-31 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 pdb2v69.ent

Checks that need to be done early-on in validation

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 : 0.096
CA-only RMS fit for the two chains : 0.063

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.112
CA-only RMS fit for the two chains : 0.061

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.098
CA-only RMS fit for the two chains : 0.067

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 E

All-atom RMS fit for the two chains : 0.095
CA-only RMS fit for the two chains : 0.066

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 F

All-atom RMS fit for the two chains : 0.091
CA-only RMS fit for the two chains : 0.059

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.

4794 MME   (   1-)  I  -
4796 MME   (   1-)  J  -
4798 MME   (   1-)  K  -
4800 MME   (   1-)  L  -
4802 MME   (   1-)  M  -
4804 MME   (   1-)  N  -
4806 MME   (   1-)  O  -
4810 CAP   (1471-)  A  -
4814 CAP   (1471-)  B  -
4818 CAP   (1472-)  C  -
4823 CAP   (1476-)  D  -
4828 CAP   (1471-)  E  -
4834 CAP   (1471-)  F  -
4838 CAP   (1471-)  G  -
4848 CAP   (1471-)  H  -
4849 MME   (   1-)  P  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

3682 MET   (   2-)  I  -   N   bound to 4794 MME   (   1-)  I  -   C
3821 MET   (   2-)  J  -   N   bound to 4796 MME   (   1-)  J  -   C
3960 MET   (   2-)  K  -   N   bound to 4798 MME   (   1-)  K  -   C
4099 MET   (   2-)  L  -   N   bound to 4800 MME   (   1-)  L  -   C
4238 MET   (   2-)  M  -   N   bound to 4802 MME   (   1-)  M  -   C
4377 MET   (   2-)  N  -   N   bound to 4804 MME   (   1-)  N  -   C
4516 MET   (   2-)  O  -   N   bound to 4806 MME   (   1-)  O  -   C
4655 MET   (   2-)  P  -   N   bound to 4849 MME   (   1-)  P  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

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.

 445 LEU   ( 455-)  A
1743 MET   ( 375-)  D

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.

1841 GLU   ( 473-)  D    High
3764 ARG   (  84-)  I    High
3767 MET   (  87-)  I    High
3810 ARG   ( 130-)  I    High
3816 ASN   ( 136-)  I    High
3817 LYS   ( 137-)  I    High
3903 ARG   (  84-)  J    High
3906 MET   (  87-)  J    High
3949 ARG   ( 130-)  J    High
3954 ALA   ( 135-)  J    High
3955 ASN   ( 136-)  J    High
3956 LYS   ( 137-)  J    High
4042 ARG   (  84-)  K    High
4045 MET   (  87-)  K    High
4088 ARG   ( 130-)  K    High
4094 ASN   ( 136-)  K    High
4095 LYS   ( 137-)  K    High
4152 GLU   (  55-)  L    High
4181 ARG   (  84-)  L    High
4184 MET   (  87-)  L    High
4227 ARG   ( 130-)  L    High
4232 ALA   ( 135-)  L    High
4233 ASN   ( 136-)  L    High
4234 LYS   ( 137-)  L    High
4291 GLU   (  55-)  M    High
4320 ARG   (  84-)  M    High
4323 MET   (  87-)  M    High
4366 ARG   ( 130-)  M    High
4372 ASN   ( 136-)  M    High
4373 LYS   ( 137-)  M    High
4459 ARG   (  84-)  N    High
4462 MET   (  87-)  N    High
4505 ARG   ( 130-)  N    High
4511 ASN   ( 136-)  N    High
4512 LYS   ( 137-)  N    High
4569 GLU   (  55-)  O    High
4598 ARG   (  84-)  O    High
4601 MET   (  87-)  O    High
4644 ARG   ( 130-)  O    High
4650 ASN   ( 136-)  O    High
4651 LYS   ( 137-)  O    High
4737 ARG   (  84-)  P    High
4740 MET   (  87-)  P    High
4783 ARG   ( 130-)  P    High
4789 ASN   ( 136-)  P    High
4790 LYS   ( 137-)  P    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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

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: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

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
 637 ARG   ( 187-)  B
1095 ARG   ( 187-)  C
1555 ARG   ( 187-)  D
2019 ARG   ( 187-)  E
2480 ARG   ( 187-)  F
2941 ARG   ( 187-)  G
3399 ARG   ( 187-)  H

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
 343 TYR   ( 353-)  A
 553 TYR   ( 103-)  B
 803 TYR   ( 353-)  B
1011 TYR   ( 103-)  C
1261 TYR   ( 353-)  C
1392 TYR   (  24-)  D
1721 TYR   ( 353-)  D
1935 TYR   ( 103-)  E
2185 TYR   ( 353-)  E
2396 TYR   ( 103-)  F
2646 TYR   ( 353-)  F
2857 TYR   ( 103-)  G
3107 TYR   ( 353-)  G
3565 TYR   ( 353-)  H
3731 TYR   (  51-)  I
3747 TYR   (  67-)  I
3784 TYR   ( 104-)  I
3870 TYR   (  51-)  J
3886 TYR   (  67-)  J
3923 TYR   ( 104-)  J
4009 TYR   (  51-)  K
4025 TYR   (  67-)  K
4062 TYR   ( 104-)  K
4148 TYR   (  51-)  L
4164 TYR   (  67-)  L
4287 TYR   (  51-)  M
4303 TYR   (  67-)  M
4340 TYR   ( 104-)  M
4426 TYR   (  51-)  N
4442 TYR   (  67-)  N
4479 TYR   ( 104-)  N
4565 TYR   (  51-)  O
4581 TYR   (  67-)  O
4704 TYR   (  51-)  P
4720 TYR   (  67-)  P

Warning: Phenylalanine convention problem

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

 459 PHE   ( 469-)  A
 919 PHE   ( 469-)  B
1119 PHE   ( 211-)  C
1770 PHE   ( 402-)  D
2762 PHE   ( 469-)  F
3223 PHE   ( 469-)  G
3692 PHE   (  12-)  I
3695 PHE   (  15-)  I
3724 PHE   (  44-)  I
3740 PHE   (  60-)  I
3780 PHE   ( 100-)  I
3801 PHE   ( 121-)  I
3812 PHE   ( 132-)  I
3831 PHE   (  12-)  J
3834 PHE   (  15-)  J
3863 PHE   (  44-)  J
3879 PHE   (  60-)  J
3919 PHE   ( 100-)  J
3940 PHE   ( 121-)  J
3951 PHE   ( 132-)  J
3970 PHE   (  12-)  K
3973 PHE   (  15-)  K
4002 PHE   (  44-)  K
4018 PHE   (  60-)  K
4058 PHE   ( 100-)  K
And so on for a total of 62 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.

  76 ASP   (  86-)  A
 536 ASP   (  86-)  B
 994 ASP   (  86-)  C
1454 ASP   (  86-)  D
1918 ASP   (  86-)  E
2379 ASP   (  86-)  F
2840 ASP   (  86-)  G
3298 ASP   (  86-)  H
3811 ASP   ( 131-)  I
3950 ASP   ( 131-)  J
4089 ASP   ( 131-)  K
4228 ASP   ( 131-)  L
4367 ASP   ( 131-)  M
4506 ASP   ( 131-)  N
4645 ASP   ( 131-)  O
4784 ASP   ( 131-)  P

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
 538 GLU   (  88-)  B
 709 GLU   ( 259-)  B
 910 GLU   ( 460-)  B
 996 GLU   (  88-)  C
1368 GLU   ( 460-)  C
1456 GLU   (  88-)  D
1627 GLU   ( 259-)  D
1828 GLU   ( 460-)  D
1920 GLU   (  88-)  E
2292 GLU   ( 460-)  E
2381 GLU   (  88-)  F
2753 GLU   ( 460-)  F
2842 GLU   (  88-)  G
3214 GLU   ( 460-)  G
3300 GLU   (  88-)  H
3672 GLU   ( 460-)  H
3726 GLU   (  46-)  I
3735 GLU   (  55-)  I
3865 GLU   (  46-)  J
3874 GLU   (  55-)  J
4004 GLU   (  46-)  K
4013 GLU   (  55-)  K
4143 GLU   (  46-)  L
4152 GLU   (  55-)  L
4282 GLU   (  46-)  M
4291 GLU   (  55-)  M
4421 GLU   (  46-)  N
4430 GLU   (  55-)  N
4560 GLU   (  46-)  O
4569 GLU   (  55-)  O
4699 GLU   (  46-)  P
4708 GLU   (  55-)  P

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
 651 KCX   ( 201-)  B      CH     CX
 651 KCX   ( 201-)  B      OX1    OQ1
 651 KCX   ( 201-)  B      OX2    OQ2
1109 KCX   ( 201-)  C      CH     CX
1109 KCX   ( 201-)  C      OX1    OQ1
1109 KCX   ( 201-)  C      OX2    OQ2
1569 KCX   ( 201-)  D      CH     CX
1569 KCX   ( 201-)  D      OX1    OQ1
1569 KCX   ( 201-)  D      OX2    OQ2
2033 KCX   ( 201-)  E      CH     CX
2033 KCX   ( 201-)  E      OX1    OQ1
2033 KCX   ( 201-)  E      OX2    OQ2
2494 KCX   ( 201-)  F      CH     CX
2494 KCX   ( 201-)  F      OX1    OQ1
2494 KCX   ( 201-)  F      OX2    OQ2
2955 KCX   ( 201-)  G      CH     CX
2955 KCX   ( 201-)  G      OX1    OQ1
2955 KCX   ( 201-)  G      OX2    OQ2
3413 KCX   ( 201-)  H      CH     CX
3413 KCX   ( 201-)  H      OX1    OQ1
3413 KCX   ( 201-)  H      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

 |  0.997687 -0.000009  0.000065|
 | -0.000009  0.998584  0.000007|
 |  0.000065  0.000007  0.998548|
Proposed new scale matrix

 |  0.008773  0.000000  0.000958|
 |  0.000000  0.005920  0.000000|
 |  0.000000  0.000000  0.007344|
With corresponding cell

    A    = 113.983  B   = 168.908  C    = 136.981
    Alpha=  90.002  Beta=  96.231  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 114.242  B   = 169.140  C    = 137.179
    Alpha=  90.000  Beta=  96.240  Gamma=  90.000

Variance: 488.972
(Under-)estimated Z-score: 16.297

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.

 284 HIS   ( 294-)  A      CG   ND1  CE1 109.71    4.1
 744 HIS   ( 294-)  B      CG   ND1  CE1 109.63    4.0
 775 HIS   ( 325-)  B      C    CA   CB  102.44   -4.0
 819 SMC   ( 369-)  B      N    CA   CB  103.21   -4.3
1146 HIS   ( 238-)  C      CG   ND1  CE1 109.70    4.1
1175 HIS   ( 267-)  C      CG   ND1  CE1 109.74    4.1
1235 HIS   ( 327-)  C      CG   ND1  CE1 109.69    4.1
1695 HIS   ( 327-)  D      CG   ND1  CE1 109.90    4.3
1737 SMC   ( 369-)  D      N    CA   CB  101.83   -5.1
1839 THR   ( 471-)  D      N    CA   CB  117.55    4.1
2159 HIS   ( 327-)  E      CG   ND1  CE1 109.69    4.1
2531 HIS   ( 238-)  F      CG   ND1  CE1 109.90    4.3
3061 HIS   ( 307-)  G      CG   ND1  CE1 109.61    4.0
3506 HIS   ( 294-)  H      CG   ND1  CE1 109.81    4.2
3510 HIS   ( 298-)  H      CG   ND1  CE1 109.71    4.1
3581 SMC   ( 369-)  H      N    CA   CB  102.82   -4.5
3688 ASN   (   8-)  I      N    CA   C    94.38   -6.0
3827 ASN   (   8-)  J      N    CA   C    96.71   -5.2
3966 ASN   (   8-)  K      N    CA   C    95.91   -5.5
4104 VAL   (   7-)  L      C    CA   CB  102.14   -4.2
4105 ASN   (   8-)  L      N    CA   C    93.04   -6.5
4244 ASN   (   8-)  M      N    CA   C    93.96   -6.2
4383 ASN   (   8-)  N      N    CA   C    96.73   -5.2
4522 ASN   (   8-)  O      N    CA   C    94.37   -6.0
4661 ASN   (   8-)  P      N    CA   C    94.85   -5.8

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.

  76 ASP   (  86-)  A
  78 GLU   (  88-)  A
 177 ARG   ( 187-)  A
 450 GLU   ( 460-)  A
 536 ASP   (  86-)  B
 538 GLU   (  88-)  B
 637 ARG   ( 187-)  B
 709 GLU   ( 259-)  B
 910 GLU   ( 460-)  B
 994 ASP   (  86-)  C
 996 GLU   (  88-)  C
1095 ARG   ( 187-)  C
1368 GLU   ( 460-)  C
1454 ASP   (  86-)  D
1456 GLU   (  88-)  D
1555 ARG   ( 187-)  D
1627 GLU   ( 259-)  D
1828 GLU   ( 460-)  D
1918 ASP   (  86-)  E
1920 GLU   (  88-)  E
2019 ARG   ( 187-)  E
2292 GLU   ( 460-)  E
2379 ASP   (  86-)  F
2381 GLU   (  88-)  F
2480 ARG   ( 187-)  F
And so on for a total of 58 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

4105 ASN   (   8-)  L    6.12
4244 ASN   (   8-)  M    5.82
4522 ASN   (   8-)  O    5.68
3688 ASN   (   8-)  I    5.68
4661 ASN   (   8-)  P    5.52
3966 ASN   (   8-)  K    5.18
3827 ASN   (   8-)  J    4.91
4383 ASN   (   8-)  N    4.91
1718 ARG   ( 350-)  D    4.18

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.

1839 THR   ( 471-)  D    -2.6
3262 PRO   (  50-)  H    -2.6
1418 PRO   (  50-)  D    -2.6
4042 ARG   (  84-)  K    -2.6
4181 ARG   (  84-)  L    -2.6
3764 ARG   (  84-)  I    -2.6
2532 TYR   ( 239-)  F    -2.6
4459 ARG   (  84-)  N    -2.6
2804 PRO   (  50-)  G    -2.5
3903 ARG   (  84-)  J    -2.5
4737 ARG   (  84-)  P    -2.5
4320 ARG   (  84-)  M    -2.5
4598 ARG   (  84-)  O    -2.5
2071 TYR   ( 239-)  E    -2.5
 229 TYR   ( 239-)  A    -2.4
4707 ASN   (  54-)  P    -2.4
 958 PRO   (  50-)  C    -2.3
4151 ASN   (  54-)  L    -2.3
4290 ASN   (  54-)  M    -2.3
4109 PHE   (  12-)  L    -2.3
3568 LYS   ( 356-)  H    -2.3
  40 PRO   (  50-)  A    -2.3
3734 ASN   (  54-)  I    -2.3
4012 ASN   (  54-)  K    -2.3
3873 ASN   (  54-)  J    -2.3
And so on for a total of 123 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.

  52 SER   (  62-)  A  Poor phi/psi
  76 ASP   (  86-)  A  Poor phi/psi
  97 LEU   ( 107-)  A  omega poor
 153 ASN   ( 163-)  A  Poor phi/psi
 165 LYS   ( 175-)  A  PRO omega poor
 189 PHE   ( 199-)  A  omega poor
 197 ASN   ( 207-)  A  Poor phi/psi
 287 MET   ( 297-)  A  Poor phi/psi
 321 VAL   ( 331-)  A  Poor phi/psi
 340 ARG   ( 350-)  A  omega poor
 360 SER   ( 370-)  A  Poor phi/psi
 454 GLU   ( 464-)  A  omega poor
 512 SER   (  62-)  B  Poor phi/psi
 513 THR   (  63-)  B  omega poor
 531 LYS   (  81-)  B  omega poor
 533 ARG   (  83-)  B  omega poor
 536 ASP   (  86-)  B  Poor phi/psi
 557 LEU   ( 107-)  B  omega poor
 613 ASN   ( 163-)  B  Poor phi/psi
 617 ARG   ( 167-)  B  Poor phi/psi
 625 LYS   ( 175-)  B  PRO omega poor
 649 PHE   ( 199-)  B  omega poor
 657 ASN   ( 207-)  B  Poor phi/psi
 747 MET   ( 297-)  B  Poor phi/psi
 780 THR   ( 330-)  B  omega poor
And so on for a total of 200 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.153

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.

3201 SER   ( 447-)  G    0.35
 729 SER   ( 279-)  B    0.36
3491 SER   ( 279-)  H    0.37
 269 SER   ( 279-)  A    0.37
1187 SER   ( 279-)  C    0.37
2111 SER   ( 279-)  E    0.38
 349 SER   ( 359-)  A    0.38
 897 SER   ( 447-)  B    0.38
1267 SER   ( 359-)  C    0.38
1815 SER   ( 447-)  D    0.38
2279 SER   ( 447-)  E    0.38
 437 SER   ( 447-)  A    0.39
2740 SER   ( 447-)  F    0.40

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!

   3 PHE   (  13-)  A      0
   5 ALA   (  15-)  A      0
   8 LYS   (  18-)  A      0
  13 THR   (  23-)  A      0
  14 TYR   (  24-)  A      0
  15 TYR   (  25-)  A      0
  16 THR   (  26-)  A      0
  19 TYR   (  29-)  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
  57 THR   (  67-)  A      0
  60 TRP   (  70-)  A      0
  64 LEU   (  74-)  A      0
  65 THR   (  75-)  A      0
  75 TYR   (  85-)  A      0
  76 ASP   (  86-)  A      0
  81 PRO   (  91-)  A      0
  83 GLU   (  93-)  A      0
  84 ASP   (  94-)  A      0
  85 ASN   (  95-)  A      0
  94 HYP   ( 104-)  A      0
 100 GLU   ( 110-)  A      0
And so on for a total of 1873 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!

2169 GLY   ( 337-)  E   2.20   18
3549 GLY   ( 337-)  H   2.12   15
2630 GLY   ( 337-)  F   2.11   16
 327 GLY   ( 337-)  A   2.09   15
1245 GLY   ( 337-)  C   2.09   16
1705 GLY   ( 337-)  D   1.99   16
3091 GLY   ( 337-)  G   1.95   14
 855 GLY   ( 405-)  B   1.72   80
3159 GLY   ( 405-)  G   1.69   80
1313 GLY   ( 405-)  C   1.63   80
 395 GLY   ( 405-)  A   1.55   80
2698 GLY   ( 405-)  F   1.54   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]

1059 HYP   ( 151-)  C    0.47 HIGH
1544 PRO   ( 176-)  D    0.19 LOW
4672 PRO   (  19-)  P    0.19 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  -124.1 half-chair C-delta/C-gamma (-126 degrees)
  40 PRO   (  50-)  A  -156.4 half-chair N/C-delta (-162 degrees)
  79 PRO   (  89-)  A    40.5 envelop C-delta (36 degrees)
 496 PRO   (  46-)  B  -126.8 half-chair C-delta/C-gamma (-126 degrees)
 499 PRO   (  49-)  B  -112.6 envelop C-gamma (-108 degrees)
 500 PRO   (  50-)  B  -148.9 envelop C-delta (-144 degrees)
 539 PRO   (  89-)  B    38.2 envelop C-delta (36 degrees)
 954 PRO   (  46-)  C  -127.9 half-chair C-delta/C-gamma (-126 degrees)
 958 PRO   (  50-)  C  -162.6 half-chair N/C-delta (-162 degrees)
 997 PRO   (  89-)  C    44.1 envelop C-delta (36 degrees)
1414 PRO   (  46-)  D  -126.1 half-chair C-delta/C-gamma (-126 degrees)
1418 PRO   (  50-)  D  -152.6 envelop C-delta (-144 degrees)
1457 PRO   (  89-)  D    45.7 half-chair C-delta/C-gamma (54 degrees)
1459 PRO   (  91-)  D  -117.2 half-chair C-delta/C-gamma (-126 degrees)
1878 PRO   (  46-)  E  -117.8 half-chair C-delta/C-gamma (-126 degrees)
1881 PRO   (  49-)  E  -112.2 envelop C-gamma (-108 degrees)
1882 PRO   (  50-)  E  -152.9 envelop C-delta (-144 degrees)
1921 PRO   (  89-)  E    41.2 envelop C-delta (36 degrees)
1974 PRO   ( 142-)  E   102.4 envelop C-beta (108 degrees)
2339 PRO   (  46-)  F  -124.5 half-chair C-delta/C-gamma (-126 degrees)
2343 PRO   (  50-)  F  -157.6 half-chair N/C-delta (-162 degrees)
2382 PRO   (  89-)  F    37.4 envelop C-delta (36 degrees)
2800 PRO   (  46-)  G  -127.5 half-chair C-delta/C-gamma (-126 degrees)
2804 PRO   (  50-)  G  -174.8 envelop N (180 degrees)
3017 PRO   ( 263-)  G   -65.7 envelop C-beta (-72 degrees)
3258 PRO   (  46-)  H  -123.5 half-chair C-delta/C-gamma (-126 degrees)
3262 PRO   (  50-)  H  -151.6 envelop C-delta (-144 degrees)
3301 PRO   (  89-)  H    36.0 envelop C-delta (36 degrees)
3303 PRO   (  91-)  H  -112.0 envelop C-gamma (-108 degrees)
3720 PRO   (  40-)  I    30.1 envelop C-delta (36 degrees)
3814 PRO   ( 134-)  I  -116.0 envelop C-gamma (-108 degrees)
3859 PRO   (  40-)  J    22.3 half-chair N/C-delta (18 degrees)
3953 PRO   ( 134-)  J  -118.8 half-chair C-delta/C-gamma (-126 degrees)
3998 PRO   (  40-)  K    21.5 half-chair N/C-delta (18 degrees)
4137 PRO   (  40-)  L    35.2 envelop C-delta (36 degrees)
4231 PRO   ( 134-)  L  -112.3 envelop C-gamma (-108 degrees)
4255 PRO   (  19-)  M    50.0 half-chair C-delta/C-gamma (54 degrees)
4276 PRO   (  40-)  M    48.9 half-chair C-delta/C-gamma (54 degrees)
4370 PRO   ( 134-)  M  -115.0 envelop C-gamma (-108 degrees)
4415 PRO   (  40-)  N    21.0 half-chair N/C-delta (18 degrees)
4509 PRO   ( 134-)  N  -119.6 half-chair C-delta/C-gamma (-126 degrees)
4554 PRO   (  40-)  O    22.4 half-chair N/C-delta (18 degrees)
4648 PRO   ( 134-)  O  -114.9 envelop C-gamma (-108 degrees)
4693 PRO   (  40-)  P    23.0 half-chair N/C-delta (18 degrees)
4787 PRO   ( 134-)  P  -115.0 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

4655 MET   (   2-)  P      N    <->  4849 MME   (   1-)  P      C    1.37    1.33  INTRA BF
3203 CYS   ( 449-)  G      SG   <->  3213 CYS   ( 459-)  G      SG   0.83    2.62  INTRA BF
2742 CYS   ( 449-)  F      SG   <->  2752 CYS   ( 459-)  F      SG   0.79    2.66  INTRA BF
1357 CYS   ( 449-)  C      SG   <->  1367 CYS   ( 459-)  C      SG   0.77    2.68  INTRA BF
3661 CYS   ( 449-)  H      SG   <->  3671 CYS   ( 459-)  H      SG   0.77    2.68  INTRA BF
4655 MET   (   2-)  P      CA   <->  4849 MME   (   1-)  P      C    0.75    2.45  INTRA BF
 899 CYS   ( 449-)  B      SG   <->   909 CYS   ( 459-)  B      SG   0.68    2.77  INTRA BF
1817 CYS   ( 449-)  D      SG   <->  1827 CYS   ( 459-)  D      SG   0.68    2.77  INTRA BF
 439 CYS   ( 449-)  A      SG   <->   449 CYS   ( 459-)  A      SG   0.67    2.78  INTRA BF
2281 CYS   ( 449-)  E      SG   <->  2291 CYS   ( 459-)  E      SG   0.59    2.86  INTRA BF
1526 GLU   ( 158-)  D      OE2  <->  1693 HIS   ( 325-)  D      NE2  0.53    2.17  INTRA BL
2560 HIS   ( 267-)  F      CD2  <->  2570 ASN   ( 277-)  F      ND2  0.48    2.62  INTRA BL
2451 GLU   ( 158-)  F      OE2  <->  2618 HIS   ( 325-)  F      NE2  0.44    2.26  INTRA BL
3021 HIS   ( 267-)  G      CD2  <->  3031 ASN   ( 277-)  G      ND2  0.44    2.66  INTRA BL
1066 GLU   ( 158-)  C      OE2  <->  1233 HIS   ( 325-)  C      NE2  0.44    2.26  INTRA BL
 148 GLU   ( 158-)  A      OE2  <->   315 HIS   ( 325-)  A      NE2  0.42    2.28  INTRA BL
1990 GLU   ( 158-)  E      OE2  <->  2157 HIS   ( 325-)  E      NE2  0.41    2.29  INTRA BL
3479 HIS   ( 267-)  H      CD2  <->  3489 ASN   ( 277-)  H      ND2  0.40    2.70  INTRA BL
2912 GLU   ( 158-)  G      OE2  <->  3079 HIS   ( 325-)  G      NE2  0.37    2.33  INTRA BL
 257 HIS   ( 267-)  A      CD2  <->   267 ASN   ( 277-)  A      ND2  0.36    2.74  INTRA BL
1175 HIS   ( 267-)  C      CD2  <->  1185 ASN   ( 277-)  C      ND2  0.35    2.75  INTRA BL
 608 GLU   ( 158-)  B      OE2  <->   775 HIS   ( 325-)  B      NE2  0.33    2.37  INTRA BL
 717 HIS   ( 267-)  B      CD2  <->   727 ASN   ( 277-)  B      ND2  0.33    2.77  INTRA BL
3370 GLU   ( 158-)  H      OE2  <->  3537 HIS   ( 325-)  H      NE2  0.32    2.38  INTRA BL
4306 ASN   (  70-)  M      N    <->  4862 HOH   (1001 )  M      O    0.31    2.39  INTRA BF
And so on for a total of 495 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

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.

4459 ARG   (  84-)  N      -7.43
4181 ARG   (  84-)  L      -7.40
4737 ARG   (  84-)  P      -7.28
3764 ARG   (  84-)  I      -7.21
4320 ARG   (  84-)  M      -7.10
3903 ARG   (  84-)  J      -7.09
4598 ARG   (  84-)  O      -6.96
4042 ARG   (  84-)  K      -6.83
3193 ARG   ( 439-)  G      -6.33
2271 ARG   ( 439-)  E      -6.32
1807 ARG   ( 439-)  D      -6.28
 429 ARG   ( 439-)  A      -6.27
2732 ARG   ( 439-)  F      -6.26
1347 ARG   ( 439-)  C      -6.22
3651 ARG   ( 439-)  H      -6.21
2283 TRP   ( 451-)  E      -6.16
1819 TRP   ( 451-)  D      -6.15
 901 TRP   ( 451-)  B      -6.15
1963 ARG   ( 131-)  E      -6.12
 441 TRP   ( 451-)  A      -6.11
3205 TRP   ( 451-)  G      -6.11
1359 TRP   ( 451-)  C      -6.11
2885 ARG   ( 131-)  G      -6.10
3663 TRP   ( 451-)  H      -6.08
 889 ARG   ( 439-)  B      -6.07
And so on for a total of 116 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

1376 GLU   ( 468-)  C      1378 - ASP    470- ( C)         -4.73

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

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.

3649 LEU   ( 437-)  H   -2.82
4630 VAL   ( 116-)  O   -2.80
4213 VAL   ( 116-)  L   -2.79
3511 ALA   ( 299-)  H   -2.77
2131 ALA   ( 299-)  E   -2.72
4491 VAL   ( 116-)  N   -2.70
3935 VAL   ( 116-)  J   -2.70
4769 VAL   ( 116-)  P   -2.68
3796 VAL   ( 116-)  I   -2.67
2592 ALA   ( 299-)  F   -2.67
 289 ALA   ( 299-)  A   -2.66
 557 LEU   ( 107-)  B   -2.66
1207 ALA   ( 299-)  C   -2.65
1475 LEU   ( 107-)  D   -2.65
1667 ALA   ( 299-)  D   -2.64
3053 ALA   ( 299-)  G   -2.64
4074 VAL   ( 116-)  K   -2.64
3319 LEU   ( 107-)  H   -2.63
2861 LEU   ( 107-)  G   -2.63
4352 VAL   ( 116-)  M   -2.62
1015 LEU   ( 107-)  C   -2.61
  97 LEU   ( 107-)  A   -2.59
 749 ALA   ( 299-)  B   -2.58
1939 LEU   ( 107-)  E   -2.54
2400 LEU   ( 107-)  F   -2.53

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.

3875 SER   (  56-)  J     - 3878 ARG   (  59-)  J        -1.79

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

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.

4851 HOH   (1018 )  B      O
4857 HOH   (1026 )  H      O
4857 HOH   (1039 )  H      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
 228 HIS   ( 238-)  A
 231 ASN   ( 241-)  A
 257 HIS   ( 267-)  A
 267 ASN   ( 277-)  A
 294 GLN   ( 304-)  A
 376 HIS   ( 386-)  A
 410 ASN   ( 420-)  A
 422 ASN   ( 432-)  A
 603 HIS   ( 153-)  B
 688 HIS   ( 238-)  B
 691 ASN   ( 241-)  B
 717 HIS   ( 267-)  B
 727 ASN   ( 277-)  B
 754 GLN   ( 304-)  B
 836 HIS   ( 386-)  B
 851 GLN   ( 401-)  B
 870 ASN   ( 420-)  B
 882 ASN   ( 432-)  B
1061 HIS   ( 153-)  C
1137 GLN   ( 229-)  C
1146 HIS   ( 238-)  C
1149 ASN   ( 241-)  C
1175 HIS   ( 267-)  C
1185 ASN   ( 277-)  C
And so on for a total of 114 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.

   6 GLY   (  16-)  A      N
  41 GLU   (  51-)  A      N
  55 THR   (  65-)  A      OG1
  56 TRP   (  66-)  A      NE1
  57 THR   (  67-)  A      N
  57 THR   (  67-)  A      OG1
  76 ASP   (  86-)  A      N
  86 GLN   (  96-)  A      N
  96 ASP   ( 106-)  A      N
 109 SER   ( 119-)  A      OG
 115 PHE   ( 125-)  A      N
 157 ARG   ( 167-)  A      N
 162 CYS   ( 172-)  A      N
 163 THR   ( 173-)  A      N
 165 LYS   ( 175-)  A      N
 165 LYS   ( 175-)  A      NZ
 169 GLY   ( 179-)  A      N
 197 ASN   ( 207-)  A      ND2
 201 PHE   ( 211-)  A      N
 207 ARG   ( 217-)  A      NH1
 226 LYS   ( 236-)  A      N
 229 TYR   ( 239-)  A      OH
 235 GLY   ( 245-)  A      N
 236 THR   ( 246-)  A      N
 285 ARG   ( 295-)  A      NE
And so on for a total of 487 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
 317 HIS   ( 327-)  A      ND1
 410 ASN   ( 420-)  A      OD1
 608 GLU   ( 158-)  B      OE1
 718 ASP   ( 268-)  B      OD1
 777 HIS   ( 327-)  B      ND1
 870 ASN   ( 420-)  B      OD1
1066 GLU   ( 158-)  C      OE1
1176 ASP   ( 268-)  C      OD1
1176 ASP   ( 268-)  C      OD2
1235 HIS   ( 327-)  C      ND1
1440 ASP   (  72-)  D      OD1
1526 GLU   ( 158-)  D      OE2
1636 ASP   ( 268-)  D      OD1
1695 HIS   ( 327-)  D      ND1
1788 ASN   ( 420-)  D      OD1
1841 GLU   ( 473-)  D      OE1
1904 ASP   (  72-)  E      OD1
1990 GLU   ( 158-)  E      OE1
2099 HIS   ( 267-)  E      NE2
2100 ASP   ( 268-)  E      OD1
2100 ASP   ( 268-)  E      OD2
2159 HIS   ( 327-)  E      ND1
2451 GLU   ( 158-)  F      OE1
2561 ASP   ( 268-)  F      OD1
2561 ASP   ( 268-)  F      OD2
2585 HIS   ( 292-)  F      NE2
2713 ASN   ( 420-)  F      OD1
2912 GLU   ( 158-)  G      OE1
3022 ASP   ( 268-)  G      OD1
3022 ASP   ( 268-)  G      OD2
3081 HIS   ( 327-)  G      ND1
3272 GLU   (  60-)  H      OE1
3284 ASP   (  72-)  H      OD1
3480 ASP   ( 268-)  H      OD1
3480 ASP   ( 268-)  H      OD2
3539 HIS   ( 327-)  H      ND1
3703 ASP   (  23-)  I      OD1
3811 ASP   ( 131-)  I      OD1
3950 ASP   ( 131-)  J      OD1
4089 ASP   ( 131-)  K      OD1
4384 ASN   (   9-)  N      OD1
4506 ASP   ( 131-)  N      OD1
4523 ASN   (   9-)  O      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 213 GLU   ( 223-)  A   H-bonding suggests Gln
 258 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 718 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 752 ASP   ( 302-)  B   H-bonding suggests Asn
1131 GLU   ( 223-)  C   H-bonding suggests Gln
1176 ASP   ( 268-)  C   H-bonding suggests Asn
1210 ASP   ( 302-)  C   H-bonding suggests Asn
1591 GLU   ( 223-)  D   H-bonding suggests Gln
1636 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
1884 GLU   (  52-)  E   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
2100 ASP   ( 268-)  E   H-bonding suggests Asn
2134 ASP   ( 302-)  E   H-bonding suggests Asn
2453 ASP   ( 160-)  F   H-bonding suggests Asn
2516 GLU   ( 223-)  F   H-bonding suggests Gln
2561 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
2977 GLU   ( 223-)  G   H-bonding suggests Gln
3022 ASP   ( 268-)  G   H-bonding suggests Asn
3056 ASP   ( 302-)  G   H-bonding suggests Asn
3480 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
3514 ASP   ( 302-)  H   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 :  -0.888
  2nd generation packing quality :  -0.475
  Ramachandran plot appearance   :  -1.855
  chi-1/chi-2 rotamer normality  :  -3.153 (poor)
  Backbone conformation          :  -0.390

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.561 (tight)
  Bond angles                    :   0.683
  Omega angle restraints         :   1.107
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.674
  B-factor distribution          :   0.327
  Inside/Outside distribution    :   1.051

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :   1.1
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.561 (tight)
  Bond angles                    :   0.683
  Omega angle restraints         :   1.107
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.674
  B-factor distribution          :   0.327
  Inside/Outside distribution    :   1.051
==============

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.