WHAT IF Check report

This file was created 2013-12-10 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb4fm5.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 : 0.301
CA-only RMS fit for the two chains : 0.107

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 : 0.194
CA-only RMS fit for the two chains : 0.091

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 : 0.309
CA-only RMS fit for the two chains : 0.101

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.297
CA-only RMS fit for the two chains : 0.105

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.265
CA-only RMS fit for the two chains : 0.093

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Warning: 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.

2217 BOG   ( 701-)  A  -
2218 BOG   ( 702-)  A  -
2219 DF0   ( 706-)  A  -
2220 BOG   ( 701-)  B  -
2222 DF0   ( 705-)  B  -
2223 BOG   ( 701-)  C  -
2224 BOG   ( 702-)  C  -
2226 DF0   ( 706-)  C  -
2229 DF0   ( 705-)  D  -
2230 BOG   ( 701-)  D  -

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.

2210 NAG   ( 704-)  A  -   O4  bound to 2209 NAG   ( 703-)  A  -   C1
2212 NAG   ( 703-)  B  -   O4  bound to 2211 NAG   ( 702-)  B  -   C1
2214 NAG   ( 704-)  C  -   O4  bound to 2213 NAG   ( 703-)  C  -   C1
2216 NAG   ( 703-)  D  -   O4  bound to 2215 NAG   ( 702-)  D  -   C1

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

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

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.

  76 PHE   ( 107-)  A    High
 155 GLU   ( 186-)  A    High
 397 ARG   ( 428-)  A    High
 552 GLN   ( 583-)  A    High
 628 PHE   ( 107-)  B    High
 691 GLU   ( 170-)  B    High
 781 GLU   ( 260-)  B    High
 789 ASP   ( 268-)  B    High
 802 GLU   ( 281-)  B    High
 930 TYR   ( 409-)  B    High
1180 PHE   ( 107-)  C    High
1259 GLU   ( 186-)  C    High
1656 GLN   ( 583-)  C    High
1707 LYS   (  82-)  D    High
1732 PHE   ( 107-)  D    High
1905 PRO   ( 280-)  D    High
1906 GLU   ( 281-)  D    High
2034 TYR   ( 409-)  D    High
2208 GLN   ( 583-)  D    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

Nomenclature related problems

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.

 145 GLU   ( 176-)  A
 155 GLU   ( 186-)  A
 241 GLU   ( 272-)  A
 291 GLU   ( 322-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 385 GLU   ( 416-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 493 GLU   ( 524-)  A
 697 GLU   ( 176-)  B
 793 GLU   ( 272-)  B
 843 GLU   ( 322-)  B
 847 GLU   ( 326-)  B
 860 GLU   ( 339-)  B
 919 GLU   ( 398-)  B
 937 GLU   ( 416-)  B
 978 GLU   ( 457-)  B
1007 GLU   ( 486-)  B
1011 GLU   ( 490-)  B
1023 GLU   ( 502-)  B
1045 GLU   ( 524-)  B
1249 GLU   ( 176-)  C
1345 GLU   ( 272-)  C
1395 GLU   ( 322-)  C
1412 GLU   ( 339-)  C
1471 GLU   ( 398-)  C
1489 GLU   ( 416-)  C
1530 GLU   ( 457-)  C
1559 GLU   ( 486-)  C
1563 GLU   ( 490-)  C
1575 GLU   ( 502-)  C
1597 GLU   ( 524-)  C
1801 GLU   ( 176-)  D
1897 GLU   ( 272-)  D
1947 GLU   ( 322-)  D
1951 GLU   ( 326-)  D
1964 GLU   ( 339-)  D
2041 GLU   ( 416-)  D
2082 GLU   ( 457-)  D
2111 GLU   ( 486-)  D
2115 GLU   ( 490-)  D
2127 GLU   ( 502-)  D
2149 GLU   ( 524-)  D

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 102 HIS   ( 133-)  A      CG   CD2   1.41    4.7
 195 HIS   ( 226-)  A      CG   CD2   1.40    4.1
 325 HIS   ( 356-)  A      CG   CD2   1.40    4.4
 684 MET   ( 163-)  B      C    O     1.14   -4.6
 728 HIS   ( 207-)  B      CG   CD2   1.41    4.6
 735 HIS   ( 214-)  B      CG   CD2   1.40    4.1
 872 HIS   ( 351-)  B      CG   CD2   1.40    4.0
1287 HIS   ( 214-)  C      CG   CD2   1.40    4.4
1424 HIS   ( 351-)  C      CG   CD2   1.42    5.4
1470 ILE   ( 397-)  C      C    O     1.14   -4.6
1490 HIS   ( 417-)  C      CG   CD2   1.40    4.3
1646 LYS   ( 573-)  C      C    O     1.12   -5.4
1758 HIS   ( 133-)  D      CG   CD2   1.40    4.1
1772 TYR   ( 147-)  D      CG   CD1   1.27   -5.7
1772 TYR   ( 147-)  D      CG   CD2   1.27   -5.8
1772 TYR   ( 147-)  D      CE1  CZ    1.24   -5.9
1772 TYR   ( 147-)  D      CE2  CZ    1.27   -4.4
1857 HIS   ( 232-)  D      CG   CD2   1.40    4.4
1867 HIS   ( 242-)  D      CG   CD2   1.41    4.5
1945 HIS   ( 320-)  D      CG   CD2   1.40    4.0
1973 TYR   ( 348-)  D      CG   CD1   1.29   -4.7
1973 TYR   ( 348-)  D      CG   CD2   1.26   -6.1
1973 TYR   ( 348-)  D      CE1  CZ    1.24   -5.6
2199 GLY   ( 574-)  D      C    O     1.11   -6.0

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999638 -0.000039 -0.000059|
 | -0.000039  0.997591 -0.000076|
 | -0.000059 -0.000076  0.998815|
Proposed new scale matrix

 |  0.005508  0.000000  0.000000|
 |  0.000000  0.007387  0.000000|
 |  0.000000  0.000000  0.007999|
With corresponding cell

    A    = 181.554  B   = 135.377  C    = 125.008
    Alpha=  90.001  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 181.632  B   = 135.696  C    = 125.150
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 149.306
(Under-)estimated Z-score: 9.005

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.

  12 ARG   (  43-)  A      CG   CD   NE  121.07    6.2
 101 VAL   ( 132-)  A      N    CA   CB  118.64    4.8
 132 MET   ( 163-)  A      N    CA   C    97.40   -4.9
 195 HIS   ( 226-)  A      CG   ND1  CE1 109.78    4.2
 211 HIS   ( 242-)  A      CG   ND1  CE1 109.97    4.4
 238 THR   ( 269-)  A      C    CA   CB  102.03   -4.2
 346 ILE   ( 377-)  A      C    CA   CB  119.24    4.8
 399 ILE   ( 430-)  A      N    CA   CB  118.06    4.4
 547 THR   ( 578-)  A      C    CA   CB  101.95   -4.3
 564 ARG   (  43-)  B      CG   CD   NE  119.71    5.4
 728 HIS   ( 207-)  B      CG   ND1  CE1 110.00    4.4
 763 HIS   ( 242-)  B      CG   ND1  CE1 109.93    4.3
 799 HIS   ( 278-)  B      CG   ND1  CE1 109.66    4.1
 877 HIS   ( 356-)  B      CG   ND1  CE1 109.71    4.1
 898 ILE   ( 377-)  B      C    CA   CB  118.86    4.6
 951 ILE   ( 430-)  B      N    CA   CB  102.30   -4.8
1094 LYS   ( 573-)  B      CA   CB   CG  124.22    5.1
1094 LYS   ( 573-)  B      CB   CG   CD  122.03    4.7
1116 ARG   (  43-)  C      CG   CD   NE  119.95    5.6
1162 HIS   (  89-)  C      CG   ND1  CE1 109.86    4.3
1167 HIS   (  94-)  C      CG   ND1  CE1 109.65    4.0
1236 MET   ( 163-)  C      N    CA   C    98.99   -4.4
1277 HIS   ( 204-)  C      CG   ND1  CE1 110.05    4.5
1299 HIS   ( 226-)  C      CG   ND1  CE1 109.71    4.1
1315 HIS   ( 242-)  C      CG   ND1  CE1 109.74    4.1
1450 ILE   ( 377-)  C      C    CA   CB  118.43    4.4
1470 ILE   ( 397-)  C      C    CA   CB  118.44    4.4
1471 GLU   ( 398-)  C     -O   -C    N   116.30   -4.2
1471 GLU   ( 398-)  C     -CA  -C    N   124.62    4.2
1503 ILE   ( 430-)  C      N    CA   CB  119.35    5.2
1503 ILE   ( 430-)  C      C    CA   CB   99.79   -5.4
1591 PHE   ( 518-)  C      C    CA   CB  101.36   -4.6
1647 GLY   ( 574-)  C     -O   -C    N   116.15   -4.3
1647 GLY   ( 574-)  C     -CA  -C    N   125.38    4.6
1651 THR   ( 578-)  C      C    CA   CB  101.75   -4.4
1668 ARG   (  43-)  D      CG   CD   NE  121.88    6.7
1741 VAL   ( 116-)  D      N    CA   CB  117.40    4.1
1757 VAL   ( 132-)  D      C    CA   CB  101.60   -4.5
1772 TYR   ( 147-)  D      CA   CB   CG  121.43    4.1
1788 MET   ( 163-)  D      N    CA   C    97.29   -5.0
1832 HIS   ( 207-)  D      CG   ND1  CE1 109.71    4.1
1851 HIS   ( 226-)  D      CG   ND1  CE1 109.75    4.2
1867 HIS   ( 242-)  D      CG   ND1  CE1 109.82    4.2
2002 ILE   ( 377-)  D      C    CA   CB  118.22    4.3
2042 HIS   ( 417-)  D      CG   ND1  CE1 109.64    4.0
2055 ILE   ( 430-)  D      N    CA   CB  120.22    5.7
2055 ILE   ( 430-)  D      C    CA   CB  102.05   -4.2
2120 TYR   ( 495-)  D      N    CA   C    97.25   -5.0
2200 CYS   ( 575-)  D     -O   -C    N   115.19   -4.9
2200 CYS   ( 575-)  D      N    CA   C    94.51   -6.0

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.

 145 GLU   ( 176-)  A
 155 GLU   ( 186-)  A
 241 GLU   ( 272-)  A
 291 GLU   ( 322-)  A
 308 GLU   ( 339-)  A
 367 GLU   ( 398-)  A
 385 GLU   ( 416-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 493 GLU   ( 524-)  A
 697 GLU   ( 176-)  B
 793 GLU   ( 272-)  B
 843 GLU   ( 322-)  B
 847 GLU   ( 326-)  B
 860 GLU   ( 339-)  B
 919 GLU   ( 398-)  B
 937 GLU   ( 416-)  B
 978 GLU   ( 457-)  B
1007 GLU   ( 486-)  B
1011 GLU   ( 490-)  B
1023 GLU   ( 502-)  B
1045 GLU   ( 524-)  B
1249 GLU   ( 176-)  C
1345 GLU   ( 272-)  C
1395 GLU   ( 322-)  C
1412 GLU   ( 339-)  C
1471 GLU   ( 398-)  C
1489 GLU   ( 416-)  C
1530 GLU   ( 457-)  C
1559 GLU   ( 486-)  C
1563 GLU   ( 490-)  C
1575 GLU   ( 502-)  C
1597 GLU   ( 524-)  C
1801 GLU   ( 176-)  D
1897 GLU   ( 272-)  D
1947 GLU   ( 322-)  D
1951 GLU   ( 326-)  D
1964 GLU   ( 339-)  D
2041 GLU   ( 416-)  D
2082 GLU   ( 457-)  D
2111 GLU   ( 486-)  D
2115 GLU   ( 490-)  D
2127 GLU   ( 502-)  D
2149 GLU   ( 524-)  D

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.

2200 CYS   ( 575-)  D    6.54
2120 TYR   ( 495-)  D    5.32
 150 VAL   ( 181-)  A    4.41
1806 VAL   ( 181-)  D    4.38
1568 TYR   ( 495-)  C    4.27
 464 TYR   ( 495-)  A    4.25
1788 MET   ( 163-)  D    4.22
 132 MET   ( 163-)  A    4.19
1016 TYR   ( 495-)  B    4.10

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.

1482 TYR   ( 409-)  C    -3.8
 378 TYR   ( 409-)  A    -3.0
 585 TYR   (  64-)  B    -3.0
1689 TYR   (  64-)  D    -3.0
  33 TYR   (  64-)  A    -2.9
1168 PHE   (  95-)  C    -2.9
1137 TYR   (  64-)  C    -2.9
1720 PHE   (  95-)  D    -2.8
1668 ARG   (  43-)  D    -2.7
 616 PHE   (  95-)  B    -2.7
  12 ARG   (  43-)  A    -2.7
 671 ARG   ( 150-)  B    -2.7
 564 ARG   (  43-)  B    -2.7
  64 PHE   (  95-)  A    -2.6
1116 ARG   (  43-)  C    -2.6
2010 TYR   ( 385-)  D    -2.6
 354 TYR   ( 385-)  A    -2.6
1258 ARG   ( 185-)  C    -2.6
2017 PRO   ( 392-)  D    -2.5
1458 TYR   ( 385-)  C    -2.5
 706 ARG   ( 185-)  B    -2.5
1223 ARG   ( 150-)  C    -2.5
 154 ARG   ( 185-)  A    -2.5
1810 ARG   ( 185-)  D    -2.5
 906 TYR   ( 385-)  B    -2.5
And so on for a total of 107 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.

  11 ASN   (  42-)  A  Poor phi/psi
  12 ARG   (  43-)  A  Poor phi/psi
  29 ARG   (  60-)  A  Poor phi/psi
  64 PHE   (  95-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
  99 TYR   ( 130-)  A  omega poor
 116 TYR   ( 147-)  A  omega poor
 118 THR   ( 149-)  A  omega poor
 131 PRO   ( 162-)  A  omega poor
 188 GLY   ( 219-)  A  omega poor
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 226 ILE   ( 257-)  A  omega poor
 228 GLY   ( 259-)  A  omega poor
 239 GLN   ( 270-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
 428 LYS   ( 459-)  A  Poor phi/psi
 440 SER   ( 471-)  A  Poor phi/psi
 454 LYS   ( 485-)  A  omega poor
 484 ASP   ( 515-)  A  Poor phi/psi
 521 GLY   ( 552-)  A  omega poor
 546 PHE   ( 577-)  A  omega poor
 559 ASN   (  38-)  B  Poor phi/psi
And so on for a total of 111 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 : -3.156

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.

1744 SER   ( 119-)  D    0.36
 976 SER   ( 455-)  B    0.37
 972 SER   ( 451-)  B    0.37
 424 SER   ( 455-)  A    0.38
1528 SER   ( 455-)  C    0.38
2080 SER   ( 455-)  D    0.38
1735 SER   ( 110-)  D    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!

   8 PRO   (  39-)  A      0
   9 CYS   (  40-)  A      0
  10 GLN   (  41-)  A      0
  12 ARG   (  43-)  A      0
  18 THR   (  49-)  A      0
  22 GLN   (  53-)  A      0
  27 CYS   (  58-)  A      0
  28 THR   (  59-)  A      0
  29 ARG   (  60-)  A      0
  30 THR   (  61-)  A      0
  32 PHE   (  63-)  A      0
  33 TYR   (  64-)  A      0
  35 GLU   (  66-)  A      0
  37 CYS   (  68-)  A      0
  38 THR   (  69-)  A      0
  62 THR   (  93-)  A      0
  63 HIS   (  94-)  A      0
  64 PHE   (  95-)  A      0
  94 ASP   ( 125-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
  98 THR   ( 129-)  A      0
  99 TYR   ( 130-)  A      0
 102 HIS   ( 133-)  A      0
And so on for a total of 829 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!

 779 GLY   ( 258-)  B   2.42   17
1331 GLY   ( 258-)  C   2.41   17
1883 GLY   ( 258-)  D   2.33   18
 227 GLY   ( 258-)  A   2.32   18
1615 PRO   ( 542-)  C   1.60   15

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]

  40 PRO   (  71-)  A    0.15 LOW
  96 PRO   ( 127-)  A    0.19 LOW
 141 PRO   ( 172-)  A    0.19 LOW
 245 PRO   ( 276-)  A    0.07 LOW
 246 PRO   ( 277-)  A    0.17 LOW
 290 PRO   ( 321-)  A    0.02 LOW
 358 PRO   ( 389-)  A    0.14 LOW
 410 PRO   ( 441-)  A    0.12 LOW
 443 PRO   ( 474-)  A    0.17 LOW
 511 PRO   ( 542-)  A    0.15 LOW
 516 PRO   ( 547-)  A    0.11 LOW
 592 PRO   (  71-)  B    0.16 LOW
 648 PRO   ( 127-)  B    0.19 LOW
 693 PRO   ( 172-)  B    0.19 LOW
 797 PRO   ( 276-)  B    0.11 LOW
 798 PRO   ( 277-)  B    0.16 LOW
 842 PRO   ( 321-)  B    0.03 LOW
 910 PRO   ( 389-)  B    0.15 LOW
 962 PRO   ( 441-)  B    0.08 LOW
 995 PRO   ( 474-)  B    0.19 LOW
1063 PRO   ( 542-)  B    0.17 LOW
1068 PRO   ( 547-)  B    0.12 LOW
1144 PRO   (  71-)  C    0.17 LOW
1245 PRO   ( 172-)  C    0.16 LOW
1349 PRO   ( 276-)  C    0.10 LOW
1350 PRO   ( 277-)  C    0.16 LOW
1394 PRO   ( 321-)  C    0.02 LOW
1462 PRO   ( 389-)  C    0.12 LOW
1514 PRO   ( 441-)  C    0.13 LOW
1547 PRO   ( 474-)  C    0.19 LOW
1615 PRO   ( 542-)  C    0.16 LOW
1620 PRO   ( 547-)  C    0.12 LOW
1696 PRO   (  71-)  D    0.19 LOW
1752 PRO   ( 127-)  D    0.18 LOW
1797 PRO   ( 172-)  D    0.19 LOW
1901 PRO   ( 276-)  D    0.08 LOW
1902 PRO   ( 277-)  D    0.17 LOW
1946 PRO   ( 321-)  D    0.03 LOW
2014 PRO   ( 389-)  D    0.16 LOW
2066 PRO   ( 441-)  D    0.10 LOW
2099 PRO   ( 474-)  D    0.17 LOW
2167 PRO   ( 542-)  D    0.17 LOW
2172 PRO   ( 547-)  D    0.15 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].

  75 PRO   ( 106-)  A   100.1 envelop C-beta (108 degrees)
  97 PRO   ( 128-)  A    30.8 envelop C-delta (36 degrees)
 122 PRO   ( 153-)  A  -119.3 half-chair C-delta/C-gamma (-126 degrees)
 265 PRO   ( 296-)  A   112.4 envelop C-beta (108 degrees)
 361 PRO   ( 392-)  A   -31.8 envelop C-alpha (-36 degrees)
 649 PRO   ( 128-)  B    40.5 envelop C-delta (36 degrees)
 674 PRO   ( 153-)  B  -114.6 envelop C-gamma (-108 degrees)
 739 PRO   ( 218-)  B   -61.8 half-chair C-beta/C-alpha (-54 degrees)
 817 PRO   ( 296-)  B   110.8 envelop C-beta (108 degrees)
 913 PRO   ( 392-)  B   -31.0 envelop C-alpha (-36 degrees)
1200 PRO   ( 127-)  C   101.5 envelop C-beta (108 degrees)
1201 PRO   ( 128-)  C    25.0 half-chair N/C-delta (18 degrees)
1226 PRO   ( 153-)  C  -117.1 half-chair C-delta/C-gamma (-126 degrees)
1291 PRO   ( 218-)  C   -65.0 envelop C-beta (-72 degrees)
1353 PRO   ( 280-)  C  -112.2 envelop C-gamma (-108 degrees)
1369 PRO   ( 296-)  C   113.6 envelop C-beta (108 degrees)
1465 PRO   ( 392-)  C   -37.1 envelop C-alpha (-36 degrees)
1753 PRO   ( 128-)  D    25.3 half-chair N/C-delta (18 degrees)
1778 PRO   ( 153-)  D  -116.9 envelop C-gamma (-108 degrees)
1843 PRO   ( 218-)  D   -65.7 envelop C-beta (-72 degrees)
1921 PRO   ( 296-)  D   107.0 envelop C-beta (108 degrees)
2017 PRO   ( 392-)  D   -30.9 envelop C-alpha (-36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

1919 LEU   ( 294-)  D      CD2 <-> 1920 VAL   ( 295-)  D      CG2    1.41    1.79  INTRA BF
 919 GLU   ( 398-)  B      CG  <->  942 GLN   ( 421-)  B      NE2    0.92    2.18  INTRA BF
1289 ARG   ( 216-)  C      CG  <-> 2213 NAG   ( 703-)  C      C8     0.69    2.51  INTRA BF
2217 BOG   ( 701-)  A      C8' <-> 2231 HOH   ( 831 )  A      O      0.69    2.11  INTRA BF
1196 LEU   ( 123-)  C      O   <-> 1542 ARG   ( 469-)  C      NH2    0.68    2.02  INTRA BF
1289 ARG   ( 216-)  C      NH1 <-> 2213 NAG   ( 703-)  C      C8     0.65    2.45  INTRA BF
2228 HEM   ( 704-)  D      C1D <-> 2234 HOH   ( 814 )  D      O      0.64    2.16  INTRA BF
 644 LEU   ( 123-)  B      O   <->  990 ARG   ( 469-)  B      NH2    0.64    2.06  INTRA BL
  92 LEU   ( 123-)  A      O   <->  438 ARG   ( 469-)  A      NH2    0.64    2.06  INTRA BF
1748 LEU   ( 123-)  D      O   <-> 2094 ARG   ( 469-)  D      NH2    0.62    2.08  INTRA BL
 231 TYR   ( 262-)  A      CE2 <->  384 LEU   ( 415-)  A      CD2    0.62    2.58  INTRA BF
1767 PHE   ( 142-)  D      O   <-> 2001 ARG   ( 376-)  D      NH2    0.58    2.12  INTRA BL
2055 ILE   ( 430-)  D      CG2 <-> 2234 HOH   ( 838 )  D      O      0.56    2.24  INTRA BF
 214 ARG   ( 245-)  A      NH2 <->  295 GLU   ( 326-)  A      OE2    0.56    2.14  INTRA BL
 737 ARG   ( 216-)  B      NH1 <-> 2211 NAG   ( 702-)  B      O7     0.55    2.15  INTRA BF
 663 PHE   ( 142-)  B      O   <->  897 ARG   ( 376-)  B      NH2    0.54    2.16  INTRA BL
1349 PRO   ( 276-)  C      CG  <-> 1482 TYR   ( 409-)  C      CD2    0.54    2.66  INTRA BF
1318 ARG   ( 245-)  C      NH2 <-> 1399 GLU   ( 326-)  C      OE2    0.54    2.16  INTRA BL
 919 GLU   ( 398-)  B      CB  <->  942 GLN   ( 421-)  B      NE2    0.53    2.57  INTRA BF
1870 ARG   ( 245-)  D      NH2 <-> 1951 GLU   ( 326-)  D      OE1    0.52    2.18  INTRA BL
   8 PRO   (  39-)  A      CD  <-> 2231 HOH   ( 823 )  A      O      0.52    2.28  INTRA BF
1215 PHE   ( 142-)  C      O   <-> 1449 ARG   ( 376-)  C      NH2    0.52    2.18  INTRA BL
 183 HIS   ( 214-)  A      ND1 <-> 2231 HOH   ( 829 )  A      O      0.51    2.19  INTRA BF
 766 ARG   ( 245-)  B      NH2 <->  847 GLU   ( 326-)  B      OE1    0.50    2.20  INTRA BL
 815 LEU   ( 294-)  B      CD2 <->  816 VAL   ( 295-)  B      CG2    0.49    2.71  INTRA BF
And so on for a total of 379 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

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.

 581 ARG   (  60-)  B      -6.74
1133 ARG   (  60-)  C      -6.72
1685 ARG   (  60-)  D      -6.59
  29 ARG   (  60-)  A      -6.58
1903 HIS   ( 278-)  D      -6.45
 799 HIS   ( 278-)  B      -6.40
1351 HIS   ( 278-)  C      -6.38
 247 HIS   ( 278-)  A      -6.29
1650 PHE   ( 577-)  C      -6.08
1689 TYR   (  64-)  D      -5.84
2202 PHE   ( 577-)  D      -5.81
1810 ARG   ( 185-)  D      -5.73
2042 HIS   ( 417-)  D      -5.70
 585 TYR   (  64-)  B      -5.70
 938 HIS   ( 417-)  B      -5.68
 706 ARG   ( 185-)  B      -5.64
 154 ARG   ( 185-)  A      -5.64
1258 ARG   ( 185-)  C      -5.60
 572 PHE   (  51-)  B      -5.59
2053 ARG   ( 428-)  D      -5.54
 546 PHE   ( 577-)  A      -5.53
1348 TYR   ( 275-)  C      -5.53
1137 TYR   (  64-)  C      -5.52
 386 HIS   ( 417-)  A      -5.51
 244 TYR   ( 275-)  A      -5.50
And so on for a total of 53 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.

 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -4.73
 690 LYS   ( 169-)  B       692 - LEU    171- ( B)         -4.67
 735 HIS   ( 214-)  B       737 - ARG    216- ( B)         -4.94
1242 LYS   ( 169-)  C      1244 - LEU    171- ( C)         -4.66
1287 HIS   ( 214-)  C      1289 - ARG    216- ( C)         -4.90
1794 LYS   ( 169-)  D      1796 - LEU    171- ( D)         -4.72
1839 HIS   ( 214-)  D      1841 - ARG    216- ( D)         -4.75

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

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.

  92 LEU   ( 123-)  A   -2.69
 334 LEU   ( 365-)  A   -2.68
1990 LEU   ( 365-)  D   -2.66
1438 LEU   ( 365-)  C   -2.63
1196 LEU   ( 123-)  C   -2.63
 105 TYR   ( 136-)  A   -2.58

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

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.

2231 HOH   ( 822 )  A      O
2232 HOH   ( 825 )  B      O
2232 HOH   ( 826 )  B      O
2233 HOH   ( 821 )  C      O
2234 HOH   ( 809 )  D      O
2234 HOH   ( 814 )  D      O
2234 HOH   ( 831 )  D      O
2234 HOH   ( 839 )  D      O
2234 HOH   ( 846 )  D      O
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 2210 NAG  ( 704-) A
Bound group on Asn; dont flip  665 ASN  ( 144-) B
Bound to: 2212 NAG  ( 703-) B
Bound group on Asn; dont flip 1217 ASN  ( 144-) C
Bound to: 2214 NAG  ( 704-) C
Bound group on Asn; dont flip 1769 ASN  ( 144-) D
Bound to: 2216 NAG  ( 703-) D
Marked this atom as acceptor 2219 DF0  ( 706-) A      F
Marked this atom as acceptor 2222 DF0  ( 705-) B      F
Marked this atom as acceptor 2226 DF0  ( 706-) C      F
Marked this atom as acceptor 2229 DF0  ( 705-) D      F
Metal-coordinating Histidine residue 357 fixed to   1
Metal-coordinating Histidine residue 909 fixed to   1
Metal-coordinating Histidine residue1461 fixed to   1
Metal-coordinating Histidine residue2013 fixed to   1

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.

  69 ASN   ( 100-)  A
 173 HIS   ( 204-)  A
 621 ASN   ( 100-)  B
 942 GLN   ( 421-)  B
1277 HIS   ( 204-)  C
1351 HIS   ( 278-)  C
1494 GLN   ( 421-)  C
1654 ASN   ( 581-)  C
1725 ASN   ( 100-)  D
2206 ASN   ( 581-)  D

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.

  22 GLN   (  53-)  A      N
  55 ASN   (  86-)  A      N
  89 ARG   ( 120-)  A      NE
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      N
 107 SER   ( 138-)  A      OG
 128 CYS   ( 159-)  A      N
 135 LYS   ( 166-)  A      N
 154 ARG   ( 185-)  A      NE
 154 ARG   ( 185-)  A      NH2
 155 GLU   ( 186-)  A      N
 177 GLN   ( 208-)  A      NE2
 190 THR   ( 221-)  A      OG1
 196 GLY   ( 227-)  A      N
 217 LYS   ( 248-)  A      N
 224 GLN   ( 255-)  A      NE2
 225 VAL   ( 256-)  A      N
 251 ASN   ( 282-)  A      N
 264 VAL   ( 295-)  A      N
 266 GLY   ( 297-)  A      N
 267 LEU   ( 298-)  A      N
 326 PHE   ( 357-)  A      N
 329 LYS   ( 360-)  A      N
 343 GLN   ( 374-)  A      NE2
 357 HIS   ( 388-)  A      N
And so on for a total of 148 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.

 172 GLN   ( 203-)  A      OE1
 211 HIS   ( 242-)  A      ND1
 380 ASN   ( 411-)  A      OD1
 661 GLU   ( 140-)  B      OE2
 724 GLN   ( 203-)  B      OE1
 725 HIS   ( 204-)  B      ND1
 762 GLN   ( 241-)  B      OE1
 763 HIS   ( 242-)  B      ND1
 860 GLU   ( 339-)  B      OE2
 907 HIS   ( 386-)  B      ND1
1213 GLU   ( 140-)  C      OE2
1276 GLN   ( 203-)  C      OE1
1315 HIS   ( 242-)  C      ND1
1403 GLN   ( 330-)  C      OE1
1459 HIS   ( 386-)  C      ND1
1484 ASN   ( 411-)  C      OD1
1828 GLN   ( 203-)  D      OE1
1829 HIS   ( 204-)  D      ND1
1867 HIS   ( 242-)  D      ND1
1955 GLN   ( 330-)  D      OE1
1964 GLU   ( 339-)  D      OE2

Warning: Unusual water packing

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

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

2234 HOH   ( 815 )  D      O  1.02  K  4

Warning: Possible wrong residue type

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

 291 GLU   ( 322-)  A   H-bonding suggests Gln
 843 GLU   ( 322-)  B   H-bonding suggests Gln
1395 GLU   ( 322-)  C   H-bonding suggests Gln
1677 ASP   (  52-)  D   H-bonding suggests Asn; but Alt-Rotamer
1947 GLU   ( 322-)  D   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.505
  2nd generation packing quality :  -1.454
  Ramachandran plot appearance   :  -1.467
  chi-1/chi-2 rotamer normality  :  -3.156 (poor)
  Backbone conformation          :  -0.793

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.708
  Bond angles                    :   0.820
  Omega angle restraints         :   1.153
  Side chain planarity           :   0.654 (tight)
  Improper dihedral distribution :   0.825
  B-factor distribution          :   0.686
  Inside/Outside distribution    :   1.109

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 : 2.81


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.708
  Bond angles                    :   0.820
  Omega angle restraints         :   1.153
  Side chain planarity           :   0.654 (tight)
  Improper dihedral distribution :   0.825
  B-factor distribution          :   0.686
  Inside/Outside distribution    :   1.109
==============

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.