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 pdb2v68.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 : 0.308
CA-only RMS fit for the two chains : 0.162

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 : 0.331
CA-only RMS fit for the two chains : 0.184

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 : 0.231
CA-only RMS fit for the two chains : 0.070

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.226
CA-only RMS fit for the two chains : 0.077

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 : 0.229
CA-only RMS fit for the two chains : 0.175

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 F

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.

4851 MME   (   1-)  I  -
4853 MME   (   1-)  J  -
4855 MME   (   1-)  K  -
4857 MME   (   1-)  L  -
4859 MME   (   1-)  M  -
4861 MME   (   1-)  N  -
4863 MME   (   1-)  O  -
4867 CAP   ( 477-)  A  -
4873 CAP   ( 477-)  B  -
4879 CAP   ( 477-)  C  -
4886 CAP   ( 477-)  D  -
4892 CAP   ( 477-)  E  -
4897 CAP   ( 477-)  F  -
4904 CAP   ( 477-)  G  -
4929 CAP   ( 477-)  H  -
4930 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.

3731 MET   (   2-)  I  -   N   bound to 4851 MME   (   1-)  I  -   C
3870 MET   (   2-)  J  -   N   bound to 4853 MME   (   1-)  J  -   C
4009 MET   (   2-)  K  -   N   bound to 4855 MME   (   1-)  K  -   C
4148 MET   (   2-)  L  -   N   bound to 4857 MME   (   1-)  L  -   C
4287 MET   (   2-)  M  -   N   bound to 4859 MME   (   1-)  M  -   C
4426 MET   (   2-)  N  -   N   bound to 4861 MME   (   1-)  N  -   C
4565 MET   (   2-)  O  -   N   bound to 4863 MME   (   1-)  O  -   C
4704 MET   (   2-)  P  -   N   bound to 4930 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: 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.

2762 ARG   ( 439-)  F    0.50
3859 ARG   ( 130-)  I    0.50
3998 ARG   ( 130-)  J    0.50
4137 ARG   ( 130-)  K    0.50
4693 ARG   ( 130-)  O    0.50

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: Leucine nomenclature problem

The leucine residues listed in the table below have their C-delta-1 and C-delta-2 swapped.

 210 LEU   ( 219-)  A
 677 LEU   ( 219-)  B
1144 LEU   ( 219-)  C
1609 LEU   ( 219-)  D
2075 LEU   ( 219-)  E
2542 LEU   ( 219-)  F
3008 LEU   ( 219-)  G
3474 LEU   ( 219-)  H

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 178 ARG   ( 187-)  A
 645 ARG   ( 187-)  B
1112 ARG   ( 187-)  C
1577 ARG   ( 187-)  D
2043 ARG   ( 187-)  E
2510 ARG   ( 187-)  F
2976 ARG   ( 187-)  G
3442 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

  76 TYR   (  85-)  A
 274 TYR   ( 283-)  A
 344 TYR   ( 353-)  A
 543 TYR   (  85-)  B
 558 TYR   ( 100-)  B
 811 TYR   ( 353-)  B
1010 TYR   (  85-)  C
1278 TYR   ( 353-)  C
1493 TYR   ( 103-)  D
1941 TYR   (  85-)  E
1959 TYR   ( 103-)  E
2209 TYR   ( 353-)  E
2408 TYR   (  85-)  F
2606 TYR   ( 283-)  F
2889 TYR   ( 100-)  G
2892 TYR   ( 103-)  G
3072 TYR   ( 283-)  G
3340 TYR   (  85-)  H
3608 TYR   ( 353-)  H
3780 TYR   (  51-)  I
3796 TYR   (  67-)  I
3919 TYR   (  51-)  J
3935 TYR   (  67-)  J
4058 TYR   (  51-)  K
4074 TYR   (  67-)  K
4197 TYR   (  51-)  L
4213 TYR   (  67-)  L
4336 TYR   (  51-)  M
4352 TYR   (  67-)  M
4475 TYR   (  51-)  N
4491 TYR   (  67-)  N
4614 TYR   (  51-)  O
4630 TYR   (  67-)  O
4753 TYR   (  51-)  P
4769 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.

 393 PHE   ( 402-)  A
 460 PHE   ( 469-)  A
 860 PHE   ( 402-)  B
 927 PHE   ( 469-)  B
1327 PHE   ( 402-)  C
1394 PHE   ( 469-)  C
1792 PHE   ( 402-)  D
1859 PHE   ( 469-)  D
2258 PHE   ( 402-)  E
2325 PHE   ( 469-)  E
2725 PHE   ( 402-)  F
2792 PHE   ( 469-)  F
3191 PHE   ( 402-)  G
3258 PHE   ( 469-)  G
3657 PHE   ( 402-)  H
3724 PHE   ( 469-)  H
3741 PHE   (  12-)  I
3744 PHE   (  15-)  I
3773 PHE   (  44-)  I
3789 PHE   (  60-)  I
3829 PHE   ( 100-)  I
3861 PHE   ( 132-)  I
3880 PHE   (  12-)  J
3883 PHE   (  15-)  J
3912 PHE   (  44-)  J
And so on for a total of 65 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.

3860 ASP   ( 131-)  I
3999 ASP   ( 131-)  J
4138 ASP   ( 131-)  K
4277 ASP   ( 131-)  L
4416 ASP   ( 131-)  M
4555 ASP   ( 131-)  N
4694 ASP   ( 131-)  O
4833 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.

  79 GLU   (  88-)  A
 546 GLU   (  88-)  B
1013 GLU   (  88-)  C
1478 GLU   (  88-)  D
1944 GLU   (  88-)  E
2316 GLU   ( 460-)  E
2411 GLU   (  88-)  F
2877 GLU   (  88-)  G
3343 GLU   (  88-)  H
3775 GLU   (  46-)  I
3784 GLU   (  55-)  I
3914 GLU   (  46-)  J
3923 GLU   (  55-)  J
4053 GLU   (  46-)  K
4062 GLU   (  55-)  K
4192 GLU   (  46-)  L
4201 GLU   (  55-)  L
4331 GLU   (  46-)  M
4340 GLU   (  55-)  M
4470 GLU   (  46-)  N
4479 GLU   (  55-)  N
4609 GLU   (  46-)  O
4618 GLU   (  55-)  O
4748 GLU   (  46-)  P
4757 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.

 192 KCX   ( 201-)  A      CH     CX
 192 KCX   ( 201-)  A      OX1    OQ1
 192 KCX   ( 201-)  A      OX2    OQ2
 659 KCX   ( 201-)  B      CH     CX
 659 KCX   ( 201-)  B      OX1    OQ1
 659 KCX   ( 201-)  B      OX2    OQ2
1126 KCX   ( 201-)  C      CH     CX
1126 KCX   ( 201-)  C      OX1    OQ1
1126 KCX   ( 201-)  C      OX2    OQ2
1591 KCX   ( 201-)  D      CH     CX
1591 KCX   ( 201-)  D      OX1    OQ1
1591 KCX   ( 201-)  D      OX2    OQ2
2057 KCX   ( 201-)  E      CH     CX
2057 KCX   ( 201-)  E      OX1    OQ1
2057 KCX   ( 201-)  E      OX2    OQ2
2524 KCX   ( 201-)  F      CH     CX
2524 KCX   ( 201-)  F      OX1    OQ1
2524 KCX   ( 201-)  F      OX2    OQ2
2990 KCX   ( 201-)  G      CH     CX
2990 KCX   ( 201-)  G      OX1    OQ1
2990 KCX   ( 201-)  G      OX2    OQ2
3456 KCX   ( 201-)  H      CH     CX
3456 KCX   ( 201-)  H      OX1    OQ1
3456 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

 |  0.996336  0.000014  0.000252|
 |  0.000014  0.996797 -0.000048|
 |  0.000252 -0.000048  0.996782|
Proposed new scale matrix

 |  0.008333  0.000000  0.004375|
 |  0.000000  0.005629  0.000000|
 | -0.000002  0.000000  0.009232|
With corresponding cell

    A    = 119.983  B   = 177.650  C    = 122.326
    Alpha=  90.001  Beta= 117.685  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 120.421  B   = 178.236  C    = 122.758
    Alpha=  90.000  Beta= 117.720  Gamma=  90.000

Variance: 1825.008
(Under-)estimated Z-score: 31.485

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.

 285 HIS   ( 294-)  A      CG   ND1  CE1 109.70    4.1
 318 HIS   ( 327-)  A      CG   ND1  CE1 109.60    4.0
1252 HIS   ( 327-)  C      CG   ND1  CE1 109.62    4.0
1688 HIS   ( 298-)  D      CG   ND1  CE1 109.70    4.1
1717 HIS   ( 327-)  D      CG   ND1  CE1 109.64    4.0
1776 HIS   ( 386-)  D      CG   ND1  CE1 109.72    4.1
2561 HIS   ( 238-)  F      CG   ND1  CE1 109.60    4.0
2650 HIS   ( 327-)  F      CG   ND1  CE1 109.66    4.1
3116 HIS   ( 327-)  G      CG   ND1  CE1 109.82    4.2
3522 HIS   ( 267-)  H      CG   ND1  CE1 109.67    4.1
3549 HIS   ( 294-)  H      CG   ND1  CE1 109.66    4.1

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.

  79 GLU   (  88-)  A
 178 ARG   ( 187-)  A
 546 GLU   (  88-)  B
 645 ARG   ( 187-)  B
1013 GLU   (  88-)  C
1112 ARG   ( 187-)  C
1478 GLU   (  88-)  D
1577 ARG   ( 187-)  D
1944 GLU   (  88-)  E
2043 ARG   ( 187-)  E
2316 GLU   ( 460-)  E
2411 GLU   (  88-)  F
2510 ARG   ( 187-)  F
2877 GLU   (  88-)  G
2976 ARG   ( 187-)  G
3343 GLU   (  88-)  H
3442 ARG   ( 187-)  H
3775 GLU   (  46-)  I
3784 GLU   (  55-)  I
3860 ASP   ( 131-)  I
3914 GLU   (  46-)  J
3923 GLU   (  55-)  J
3999 ASP   ( 131-)  J
4053 GLU   (  46-)  K
4062 GLU   (  55-)  K
4138 ASP   ( 131-)  K
4192 GLU   (  46-)  L
4201 GLU   (  55-)  L
4277 ASP   ( 131-)  L
4331 GLU   (  46-)  M
4340 GLU   (  55-)  M
4416 ASP   ( 131-)  M
4470 GLU   (  46-)  N
4479 GLU   (  55-)  N
4555 ASP   ( 131-)  N
4609 GLU   (  46-)  O
4618 GLU   (  55-)  O
4694 ASP   ( 131-)  O
4748 GLU   (  46-)  P
4757 GLU   (  55-)  P
4833 ASP   ( 131-)  P

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.

3557 ASP   ( 302-)  H    4.75
2158 ASP   ( 302-)  E    4.46
1227 ASP   ( 302-)  C    4.36
3379 VAL   ( 124-)  H    4.28
 293 ASP   ( 302-)  A    4.28
 375 VAL   ( 384-)  A    4.23
 760 ASP   ( 302-)  B    4.18
2240 VAL   ( 384-)  E    4.18
1309 VAL   ( 384-)  C    4.13

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.

 939 LYS   (  14-)  C    -2.6
1870 LYS   (  14-)  E    -2.5
3269 LYS   (  14-)  H    -2.5
   5 LYS   (  14-)  A    -2.5
1404 LYS   (  14-)  D    -2.5
2803 LYS   (  14-)  G    -2.5
 472 LYS   (  14-)  B    -2.5
2337 LYS   (  14-)  F    -2.5
3866 LYS   ( 137-)  I    -2.4
3986 ILE   ( 118-)  J    -2.3
4542 ILE   ( 118-)  N    -2.3
4820 ILE   ( 118-)  P    -2.3
4693 ARG   ( 130-)  O    -2.3
4125 ILE   ( 118-)  K    -2.3
4264 ILE   ( 118-)  L    -2.3
4403 ILE   ( 118-)  M    -2.3
4291 PRO   (   6-)  M    -2.3
3847 ILE   ( 118-)  I    -2.3
4681 ILE   ( 118-)  O    -2.2
3385 LEU   ( 130-)  H    -2.2
3519 ILE   ( 264-)  H    -2.2
3053 ILE   ( 264-)  G    -2.2
3984 VAL   ( 116-)  J    -2.2
4430 PRO   (   6-)  N    -2.2
4714 PHE   (  12-)  P    -2.2
And so on for a total of 87 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   2 ALA   (  11-)  A  Poor phi/psi
   3 GLY   (  12-)  A  omega poor
  14 THR   (  23-)  A  omega poor
  26 ASP   (  35-)  A  omega poor
  32 ARG   (  41-)  A  omega poor
  53 SER   (  62-)  A  Poor phi/psi
  56 THR   (  65-)  A  omega poor
 154 ASN   ( 163-)  A  Poor phi/psi
 163 CYS   ( 172-)  A  Poor phi/psi
 166 LYS   ( 175-)  A  PRO omega poor
 190 PHE   ( 199-)  A  omega poor
 198 ASN   ( 207-)  A  Poor phi/psi
 254 PRO   ( 263-)  A  omega poor
 288 MET   ( 297-)  A  Poor phi/psi
 292 ILE   ( 301-)  A  omega poor
 322 ALA   ( 331-)  A  Poor phi/psi
 361 SER   ( 370-)  A  Poor phi/psi
 481 THR   (  23-)  B  omega poor
 493 ASP   (  35-)  B  omega poor
 499 ARG   (  41-)  B  omega poor
 520 SER   (  62-)  B  Poor phi/psi
 621 ASN   ( 163-)  B  Poor phi/psi
 633 LYS   ( 175-)  B  PRO omega poor
 657 PHE   ( 199-)  B  omega poor
 665 ASN   ( 207-)  B  Poor phi/psi
And so on for a total of 192 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.

2135 SER   ( 279-)  E    0.35
3534 SER   ( 279-)  H    0.35
1204 SER   ( 279-)  C    0.35
2602 SER   ( 279-)  F    0.36
1669 SER   ( 279-)  D    0.36
 270 SER   ( 279-)  A    0.36
 737 SER   ( 279-)  B    0.36
3068 SER   ( 279-)  G    0.37
1837 SER   ( 447-)  D    0.39
2303 SER   ( 447-)  E    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   6 ALA   (  15-)  A      0
   9 LYS   (  18-)  A      0
  14 THR   (  23-)  A      0
  15 TYR   (  24-)  A      0
  16 TYR   (  25-)  A      0
  17 THR   (  26-)  A      0
  20 TYR   (  29-)  A      0
  37 PRO   (  46-)  A      0
  52 SER   (  61-)  A      0
  53 SER   (  62-)  A      0
  54 THR   (  63-)  A      0
  57 TRP   (  66-)  A      0
  61 TRP   (  70-)  A      0
  65 LEU   (  74-)  A      0
  76 TYR   (  85-)  A      0
  77 ASP   (  86-)  A      0
  82 PRO   (  91-)  A      0
  85 ASP   (  94-)  A      0
  86 ASN   (  95-)  A      0
  87 GLN   (  96-)  A      0
  95 HYP   ( 104-)  A      0
 101 GLU   ( 110-)  A      0
 112 VAL   ( 121-)  A      0
 114 ASN   ( 123-)  A      0
 115 VAL   ( 124-)  A      0
And so on for a total of 1863 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!

2193 GLY   ( 337-)  E   2.39   11
1262 GLY   ( 337-)  C   2.38   13
3126 GLY   ( 337-)  G   2.37   16
 795 GLY   ( 337-)  B   2.36   12
1727 GLY   ( 337-)  D   2.35   17
 328 GLY   ( 337-)  A   2.35   15
2660 GLY   ( 337-)  F   2.34   15
3592 GLY   ( 337-)  H   2.27   14
1330 GLY   ( 405-)  C   1.70   80
2728 GLY   ( 405-)  F   1.64   80
3660 GLY   ( 405-)  H   1.64   80
 396 GLY   ( 405-)  A   1.63   80
1795 GLY   ( 405-)  D   1.63   80
 863 GLY   ( 405-)  B   1.59   80
2261 GLY   ( 405-)  E   1.55   80
3194 GLY   ( 405-)  G   1.53   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]

 830 PRO   ( 372-)  B    0.18 LOW
3863 PRO   ( 134-)  I    0.17 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].

  37 PRO   (  46-)  A  -124.3 half-chair C-delta/C-gamma (-126 degrees)
 504 PRO   (  46-)  B  -125.6 half-chair C-delta/C-gamma (-126 degrees)
 868 PRO   ( 410-)  B  -112.3 envelop C-gamma (-108 degrees)
 971 PRO   (  46-)  C  -122.7 half-chair C-delta/C-gamma (-126 degrees)
1335 PRO   ( 410-)  C  -112.2 envelop C-gamma (-108 degrees)
1436 PRO   (  46-)  D  -126.7 half-chair C-delta/C-gamma (-126 degrees)
1902 PRO   (  46-)  E  -123.1 half-chair C-delta/C-gamma (-126 degrees)
1998 PRO   ( 142-)  E    99.2 envelop C-beta (108 degrees)
2369 PRO   (  46-)  F  -126.2 half-chair C-delta/C-gamma (-126 degrees)
2835 PRO   (  46-)  G  -132.3 half-chair C-delta/C-gamma (-126 degrees)
3199 PRO   ( 410-)  G  -115.3 envelop C-gamma (-108 degrees)
3301 PRO   (  46-)  H  -119.6 half-chair C-delta/C-gamma (-126 degrees)
3769 PRO   (  40-)  I    51.4 half-chair C-delta/C-gamma (54 degrees)
3855 PRO   ( 126-)  I  -113.3 envelop C-gamma (-108 degrees)
3908 PRO   (  40-)  J    52.1 half-chair C-delta/C-gamma (54 degrees)
3994 PRO   ( 126-)  J  -114.7 envelop C-gamma (-108 degrees)
4047 PRO   (  40-)  K    50.2 half-chair C-delta/C-gamma (54 degrees)
4272 PRO   ( 126-)  L  -114.7 envelop C-gamma (-108 degrees)
4291 PRO   (   6-)  M   -62.1 half-chair C-beta/C-alpha (-54 degrees)
4325 PRO   (  40-)  M    50.8 half-chair C-delta/C-gamma (54 degrees)
4411 PRO   ( 126-)  M  -116.6 envelop C-gamma (-108 degrees)
4430 PRO   (   6-)  N   -59.5 half-chair C-beta/C-alpha (-54 degrees)
4464 PRO   (  40-)  N    44.6 envelop C-delta (36 degrees)
4603 PRO   (  40-)  O    42.5 envelop C-delta (36 degrees)
4689 PRO   ( 126-)  O  -113.5 envelop C-gamma (-108 degrees)
4828 PRO   ( 126-)  P  -113.7 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.

4704 MET   (   2-)  P      N    <->  4930 MME   (   1-)  P      C    1.37    1.33  INTRA B3
4704 MET   (   2-)  P      CA   <->  4930 MME   (   1-)  P      C    0.77    2.43  INTRA
1223 HIS   ( 298-)  C      ND1  <->  1227 ASP   ( 302-)  C      OD2  0.36    2.34  INTRA
2123 HIS   ( 267-)  E      CD2  <->  2133 ASN   ( 277-)  E      ND2  0.34    2.76  INTRA BL
3553 HIS   ( 298-)  H      ND1  <->  3557 ASP   ( 302-)  H      OD2  0.34    2.36  INTRA
2947 GLU   ( 158-)  G      OE2  <->  3114 HIS   ( 325-)  G      NE2  0.34    2.36  INTRA
 756 HIS   ( 298-)  B      ND1  <->   760 ASP   ( 302-)  B      OD2  0.34    2.36  INTRA
2621 HIS   ( 298-)  F      ND1  <->  2625 ASP   ( 302-)  F      OD2  0.32    2.38  INTRA
2590 HIS   ( 267-)  F      CD2  <->  2600 ASN   ( 277-)  F      ND2  0.30    2.80  INTRA BL
 289 HIS   ( 298-)  A      ND1  <->   293 ASP   ( 302-)  A      OD2  0.30    2.40  INTRA
1688 HIS   ( 298-)  D      ND1  <->  1692 ASP   ( 302-)  D      OD2  0.29    2.41  INTRA
3522 HIS   ( 267-)  H      CD2  <->  3532 ASN   ( 277-)  H      ND2  0.29    2.81  INTRA BL
2014 GLU   ( 158-)  E      OE2  <->  2181 HIS   ( 325-)  E      NE2  0.28    2.42  INTRA
 258 HIS   ( 267-)  A      CD2  <->   268 ASN   ( 277-)  A      ND2  0.28    2.82  INTRA BL
 616 GLU   ( 158-)  B      OE2  <->   783 HIS   ( 325-)  B      NE2  0.27    2.43  INTRA
1192 HIS   ( 267-)  C      CD2  <->  1202 ASN   ( 277-)  C      ND2  0.26    2.84  INTRA BL
1657 HIS   ( 267-)  D      CD2  <->  1667 ASN   ( 277-)  D      ND2  0.26    2.84  INTRA BL
 725 HIS   ( 267-)  B      CD2  <->   735 ASN   ( 277-)  B      ND2  0.26    2.84  INTRA BL
1471 LYS   (  81-)  D      NZ   <->  4934 HOH   (2043 )  D      O    0.26    2.44  INTRA
2481 GLU   ( 158-)  F      OE2  <->  2648 HIS   ( 325-)  F      NE2  0.25    2.45  INTRA
 149 GLU   ( 158-)  A      OE2  <->   316 HIS   ( 325-)  A      NE2  0.25    2.45  INTRA
 220 GLN   ( 229-)  A      NE2  <->  4931 HOH   (2122 )  A      O    0.25    2.45  INTRA BL
3393 LEU   ( 138-)  H      O    <->  3571 LYS   ( 316-)  H      NZ   0.25    2.45  INTRA BL
3416 LYS   ( 161-)  H      NZ   <->  4938 HOH   (2089 )  H      O    0.24    2.46  INTRA
4016 ASN   (   9-)  K      ND2  <->  4941 HOH   (2004 )  K      O    0.24    2.46  INTRA BL
And so on for a total of 374 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.

4369 ARG   (  84-)  M      -7.64
4230 ARG   (  84-)  L      -7.55
4786 ARG   (  84-)  P      -7.21
3952 ARG   (  84-)  J      -7.17
3813 ARG   (  84-)  I      -6.97
4647 ARG   (  84-)  O      -6.74
4508 ARG   (  84-)  N      -6.69
4091 ARG   (  84-)  K      -6.55
1364 ARG   ( 439-)  C      -5.82
3228 ARG   ( 439-)  G      -5.80
1829 ARG   ( 439-)  D      -5.78
 897 ARG   ( 439-)  B      -5.77
2295 ARG   ( 439-)  E      -5.75
3694 ARG   ( 439-)  H      -5.73
 430 ARG   ( 439-)  A      -5.65
2762 ARG   ( 439-)  F      -5.64
4640 LYS   (  77-)  O      -5.49
2803 LYS   (  14-)  G      -5.47
 472 LYS   (  14-)  B      -5.45
 939 LYS   (  14-)  C      -5.45
1870 LYS   (  14-)  E      -5.45
   5 LYS   (  14-)  A      -5.43
3240 TRP   ( 451-)  G      -5.43
1404 LYS   (  14-)  D      -5.42
4362 LYS   (  77-)  M      -5.42
And so on for a total of 94 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: 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.

2155 ALA   ( 299-)  E   -2.94
 757 ALA   ( 299-)  B   -2.86
1689 ALA   ( 299-)  D   -2.85
3554 ALA   ( 299-)  H   -2.84
2622 ALA   ( 299-)  F   -2.81
3088 ALA   ( 299-)  G   -2.80
 290 ALA   ( 299-)  A   -2.80
4679 VAL   ( 116-)  O   -2.79
1224 ALA   ( 299-)  C   -2.78
3845 VAL   ( 116-)  I   -2.77
4818 VAL   ( 116-)  P   -2.72
2293 LEU   ( 437-)  E   -2.69
3984 VAL   ( 116-)  J   -2.68
3692 LEU   ( 437-)  H   -2.68
3226 LEU   ( 437-)  G   -2.68
 428 LEU   ( 437-)  A   -2.67
2760 LEU   ( 437-)  F   -2.66
 895 LEU   ( 437-)  B   -2.65
1827 LEU   ( 437-)  D   -2.64
1362 LEU   ( 437-)  C   -2.63
1963 LEU   ( 107-)  E   -2.56
 565 LEU   ( 107-)  B   -2.56
  98 LEU   ( 107-)  A   -2.56
2896 LEU   ( 107-)  G   -2.55
2430 LEU   ( 107-)  F   -2.54
1032 LEU   ( 107-)  C   -2.53
1497 LEU   ( 107-)  D   -2.52
3362 LEU   ( 107-)  H   -2.50

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.

4932 HOH   (2162 )  B      O
4936 HOH   (2164 )  F      O
4937 HOH   (2210 )  G      O
4940 HOH   (2041 )  J      O
4945 HOH   (2038 )  O      O
ERROR. No convergence in HB2STD
Old,New value: 4922.383 4922.400

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.

 220 GLN   ( 229-)  A
 229 HIS   ( 238-)  A
 232 ASN   ( 241-)  A
 258 HIS   ( 267-)  A
 268 ASN   ( 277-)  A
 295 GLN   ( 304-)  A
 318 HIS   ( 327-)  A
 392 GLN   ( 401-)  A
 411 ASN   ( 420-)  A
 423 ASN   ( 432-)  A
 611 HIS   ( 153-)  B
 687 GLN   ( 229-)  B
 696 HIS   ( 238-)  B
 699 ASN   ( 241-)  B
 725 HIS   ( 267-)  B
 735 ASN   ( 277-)  B
 762 GLN   ( 304-)  B
 785 HIS   ( 327-)  B
 878 ASN   ( 420-)  B
 890 ASN   ( 432-)  B
1081 GLN   ( 156-)  C
1088 ASN   ( 163-)  C
1154 GLN   ( 229-)  C
1163 HIS   ( 238-)  C
1166 ASN   ( 241-)  C
And so on for a total of 133 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.

   2 ALA   (  11-)  A      N
  56 THR   (  65-)  A      OG1
  58 THR   (  67-)  A      N
  87 GLN   (  96-)  A      N
 115 VAL   ( 124-)  A      N
 158 ARG   ( 167-)  A      N
 164 THR   ( 173-)  A      OG1
 166 LYS   ( 175-)  A      N
 166 LYS   ( 175-)  A      NZ
 169 LEU   ( 178-)  A      N
 170 GLY   ( 179-)  A      N
 202 PHE   ( 211-)  A      N
 208 ARG   ( 217-)  A      NH1
 286 ARG   ( 295-)  A      NE
 286 ARG   ( 295-)  A      NH1
 294 ARG   ( 303-)  A      NE
 295 GLN   ( 304-)  A      NE2
 323 VAL   ( 332-)  A      N
 357 GLN   ( 366-)  A      NE2
 372 GLY   ( 381-)  A      N
 374 HIS   ( 383-)  A      N
 392 GLN   ( 401-)  A      NE2
 395 GLY   ( 404-)  A      N
 404 ASN   ( 413-)  A      ND2
 405 ALA   ( 414-)  A      N
And so on for a total of 248 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.

 144 HIS   ( 153-)  A      NE2
 259 ASP   ( 268-)  A      OD1
 259 ASP   ( 268-)  A      OD2
 283 HIS   ( 292-)  A      NE2
 377 HIS   ( 386-)  A      NE2
 726 ASP   ( 268-)  B      OD1
 750 HIS   ( 292-)  B      NE2
 844 HIS   ( 386-)  B      NE2
1078 HIS   ( 153-)  C      NE2
1193 ASP   ( 268-)  C      OD1
1193 ASP   ( 268-)  C      OD2
1217 HIS   ( 292-)  C      NE2
1326 GLN   ( 401-)  C      OE1
1658 ASP   ( 268-)  D      OD1
1658 ASP   ( 268-)  D      OD2
1682 HIS   ( 292-)  D      NE2
1791 GLN   ( 401-)  D      OE1
2124 ASP   ( 268-)  E      OD1
2183 HIS   ( 327-)  E      ND1
2591 ASP   ( 268-)  F      OD1
2615 HIS   ( 292-)  F      NE2
2709 HIS   ( 386-)  F      NE2
2724 GLN   ( 401-)  F      OE1
3057 ASP   ( 268-)  G      OD1
3057 ASP   ( 268-)  G      OD2
3081 HIS   ( 292-)  G      NE2
3523 ASP   ( 268-)  H      OD1
3547 HIS   ( 292-)  H      NE2

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: 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.

4931 HOH   (2125 )  A      O  0.95  K  4 NCS 4/4
4931 HOH   (2147 )  A      O  0.98  K  4 NCS 7/7
4932 HOH   (2176 )  B      O  0.95  K  4 Ion-B NCS 6/6
4933 HOH   (2111 )  C      O  0.90  K  4 NCS 4/4
4933 HOH   (2120 )  C      O  1.07  K  4 NCS 6/6
4933 HOH   (2146 )  C      O  0.99  K  4 NCS 7/7
4934 HOH   (2054 )  D      O  1.13  K  4 ION-B NCS 4/4
4934 HOH   (2138 )  D      O  0.88  K  4 NCS 7/7
4934 HOH   (2176 )  D      O  1.06  K  5 Ion-B NCS 6/6
4935 HOH   (2188 )  E      O  1.00  K  4 ION-B NCS 7/7
4935 HOH   (2192 )  E      O  0.88  K  4 NCS 4/4
4936 HOH   (2033 )  F      O  0.89  K  6 Ion-B NCS 6/6
4936 HOH   (2073 )  F      O  1.11  K  4 NCS 7/7
4936 HOH   (2137 )  F      O  1.01  K  4 NCS 7/7
4936 HOH   (2178 )  F      O  0.86  K  4 Ion-B NCS 3/3
4936 HOH   (2179 )  F      O  1.04  K  5 Ion-B NCS 7/7
4936 HOH   (2181 )  F      O  0.89  K  4 ION-B NCS 3/3
4937 HOH   (2096 )  G      O  1.09  K  4 Ion-B NCS 4/4
4938 HOH   (2052 )  H      O  0.96  K  4 Ion-B NCS 6/6
4938 HOH   (2141 )  H      O  1.01  K  4 NCS 7/7
4939 HOH   (2020 )  I      O  0.93  K  4 NCS 6/6
4939 HOH   (2048 )  I      O  0.90  K  5 NCS 7/7
4942 HOH   (2023 )  L      O  0.89  K  4 NCS 6/6
4943 HOH   (2022 )  M      O  1.01  K  4 NCS 6/6
4944 HOH   (2016 )  N      O  1.06  K  4 NCS 6/6
4945 HOH   (2016 )  O      O  1.11  K  4 NCS 6/6

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.

  43 GLU   (  52-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 151 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 259 ASP   ( 268-)  A   H-bonding suggests Asn
 510 GLU   (  52-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 726 ASP   ( 268-)  B   H-bonding suggests Asn
 977 GLU   (  52-)  C   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1193 ASP   ( 268-)  C   H-bonding suggests Asn
1227 ASP   ( 302-)  C   H-bonding suggests Asn
1442 GLU   (  52-)  D   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1550 ASP   ( 160-)  D   H-bonding suggests Asn; but Alt-Rotamer
1658 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
1908 GLU   (  52-)  E   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
2016 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
2124 ASP   ( 268-)  E   H-bonding suggests Asn
2142 ASP   ( 286-)  E   H-bonding suggests Asn
2375 GLU   (  52-)  F   H-bonding suggests Gln; Ligand-contact
2591 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
2949 ASP   ( 160-)  G   H-bonding suggests Asn; but Alt-Rotamer
3057 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
3307 GLU   (  52-)  H   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
3415 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
3523 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
3784 GLU   (  55-)  I   H-bonding suggests Gln; Ligand-contact
3923 GLU   (  55-)  J   H-bonding suggests Gln; Ligand-contact
4062 GLU   (  55-)  K   H-bonding suggests Gln; Ligand-contact
4201 GLU   (  55-)  L   H-bonding suggests Gln; Ligand-contact
4340 GLU   (  55-)  M   H-bonding suggests Gln; Ligand-contact
4479 GLU   (  55-)  N   H-bonding suggests Gln; Ligand-contact
4618 GLU   (  55-)  O   H-bonding suggests Gln; Ligand-contact
4757 GLU   (  55-)  P   H-bonding suggests Gln; Ligand-contact

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 :  -0.651
  2nd generation packing quality :  -0.153
  Ramachandran plot appearance   :  -0.666
  chi-1/chi-2 rotamer normality  :  -1.036
  Backbone conformation          :  -0.597

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.511 (tight)
  Bond angles                    :   0.639 (tight)
  Omega angle restraints         :   1.112
  Side chain planarity           :   0.430 (tight)
  Improper dihedral distribution :   0.646
  B-factor distribution          :   0.368
  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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.511 (tight)
  Bond angles                    :   0.639 (tight)
  Omega angle restraints         :   1.112
  Side chain planarity           :   0.430 (tight)
  Improper dihedral distribution :   0.646
  B-factor distribution          :   0.368
  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.