WHAT IF Check report

This file was created 2011-12-16 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 pdb3mf3.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 : 1.032
CA-only RMS fit for the two chains : 0.555

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 : 0.915
CA-only RMS fit for the two chains : 0.357

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 : 0.975
CA-only RMS fit for the two chains : 0.529

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 : 0.902
CA-only RMS fit for the two chains : 0.353

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 E

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 : 0.851
CA-only RMS fit for the two chains : 0.328

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.

1306 ACT   ( 222-)  B  -
1308 ACT   ( 222-)  B  -
1310 ACT   ( 222-)  D  -
1314 ACT   ( 222-)  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

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

Warning: Missing atoms

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

 240 GLU   (  20-)  B      CG
 240 GLU   (  20-)  B      CD
 240 GLU   (  20-)  B      OE1
 240 GLU   (  20-)  B      OE2
 241 GLU   (  21-)  B      CG
 241 GLU   (  21-)  B      CD
 241 GLU   (  21-)  B      OE1
 241 GLU   (  21-)  B      OE2
 679 ASN   (  22-)  D      CG
 679 ASN   (  22-)  D      OD1
 679 ASN   (  22-)  D      ND2
 892 GLU   (  21-)  E      CG
 892 GLU   (  21-)  E      CD
 892 GLU   (  21-)  E      OE1
 892 GLU   (  21-)  E      OE2

Warning: B-factors outside the range 0.0 - 100.0

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

  15 GLN   (  16-)  A    High
  16 ARG   (  17-)  A    High
  17 MET   (  18-)  A    High
  18 LYS   (  19-)  A    High
  19 GLU   (  20-)  A    High
  20 GLU   (  21-)  A    High
  21 ASN   (  22-)  A    High
  22 SER   (  23-)  A    High
  23 THR   (  24-)  A    High
  24 TYR   (  25-)  A    High
  26 LYS   (  27-)  A    High
  27 GLU   (  28-)  A    High
  30 ASP   (  31-)  A    High
 215 ASP   ( 216-)  A    High
 216 GLU   ( 217-)  A    High
 217 GLU   ( 218-)  A    High
 218 ASN   ( 219-)  A    High
 219 ILE   ( 220-)  A    High
 220 LEU   ( 221-)  A    High
 221 MET   (   1-)  B    High
 222 ASP   (   2-)  B    High
 236 GLN   (  16-)  B    High
 237 ARG   (  17-)  B    High
 238 MET   (  18-)  B    High
 239 LYS   (  19-)  B    High
And so on for a total of 172 lines.

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: 7

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

Nomenclature related problems

Warning: Arginine nomenclature problem

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

1069 ARG   ( 198-)  E

Warning: Tyrosine convention problem

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

  36 TYR   (  37-)  A
 232 TYR   (  12-)  B
 257 TYR   (  37-)  B
 401 TYR   ( 181-)  B
 453 TYR   (  12-)  C
 478 TYR   (  37-)  C
 622 TYR   ( 181-)  C
 682 TYR   (  25-)  D
 694 TYR   (  37-)  D
 838 TYR   ( 181-)  D
 883 TYR   (  12-)  E
 908 TYR   (  37-)  E
1124 TYR   (  37-)  F
1268 TYR   ( 181-)  F

Warning: Phenylalanine convention problem

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

  25 PHE   (  26-)  A
  74 PHE   (  75-)  A
 127 PHE   ( 128-)  A
 186 PHE   ( 187-)  A
 246 PHE   (  26-)  B
 295 PHE   (  75-)  B
 407 PHE   ( 187-)  B
 467 PHE   (  26-)  C
 516 PHE   (  75-)  C
 569 PHE   ( 128-)  C
 628 PHE   ( 187-)  C
 732 PHE   (  75-)  D
 844 PHE   ( 187-)  D
 897 PHE   (  26-)  E
 946 PHE   (  75-)  E
1058 PHE   ( 187-)  E
1113 PHE   (  26-)  F
1162 PHE   (  75-)  F
1215 PHE   ( 128-)  F
1274 PHE   ( 187-)  F

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.

   1 ASP   (   2-)  A
  30 ASP   (  31-)  A
  43 ASP   (  44-)  A
 109 ASP   ( 110-)  A
 143 ASP   ( 144-)  A
 364 ASP   ( 144-)  B
 436 ASP   ( 216-)  B
 443 ASP   (   2-)  C
 553 ASP   ( 112-)  C
 585 ASP   ( 144-)  C
 626 ASP   ( 185-)  C
 659 ASP   (   2-)  D
 801 ASP   ( 144-)  D
 842 ASP   ( 185-)  D
 981 ASP   ( 110-)  E
 983 ASP   ( 112-)  E
1015 ASP   ( 144-)  E
1056 ASP   ( 185-)  E
1089 ASP   (   2-)  F
1231 ASP   ( 144-)  F

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.

 168 GLU   ( 169-)  A
 216 GLU   ( 217-)  A
 217 GLU   ( 218-)  A
 248 GLU   (  28-)  B
 276 GLU   (  56-)  B
 279 GLU   (  59-)  B
 311 GLU   (  91-)  B
 389 GLU   ( 169-)  B
 422 GLU   ( 202-)  B
 462 GLU   (  21-)  C
 469 GLU   (  28-)  C
 497 GLU   (  56-)  C
 500 GLU   (  59-)  C
 581 GLU   ( 140-)  C
 610 GLU   ( 169-)  C
 658 GLU   ( 217-)  C
 678 GLU   (  21-)  D
 748 GLU   (  91-)  D
 856 GLU   ( 199-)  D
 899 GLU   (  28-)  E
 927 GLU   (  56-)  E
 962 GLU   (  91-)  E
1040 GLU   ( 169-)  E
1070 GLU   ( 199-)  E
1107 GLU   (  20-)  F
1178 GLU   (  91-)  F
1227 GLU   ( 140-)  F
1256 GLU   ( 169-)  F

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.

  46 VAL   (  47-)  A      CA   CB    1.64    5.6
 769 ASP   ( 112-)  D      CB   CG    1.62    4.0
1032 THR   ( 161-)  E      CA   CB    1.62    4.5
1199 ASP   ( 112-)  F      CB   CG    1.63    4.5

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

 |  0.998448 -0.000883 -0.000431|
 | -0.000883  0.998251 -0.000306|
 | -0.000431 -0.000306  0.999880|
Proposed new scale matrix

 |  0.004364  0.000004  0.000289|
 |  0.000006  0.006912  0.000002|
 |  0.000008  0.000006  0.019195|
With corresponding cell

    A    = 229.160  B   = 144.674  C    =  52.212
    Alpha=  90.028  Beta=  93.813  Gamma=  90.101

The CRYST1 cell dimensions

    A    = 229.492  B   = 144.929  C    =  52.215
    Alpha=  90.000  Beta=  93.770  Gamma=  90.000

Variance: 77.889
(Under-)estimated Z-score: 6.504

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.

 283 HIS   (  63-)  B      CG   ND1  CE1 109.63    4.0
 290 VAL   (  70-)  B      N    CA   C    99.86   -4.0
 325 HIS   ( 105-)  B      CG   ND1  CE1 109.68    4.1
 342 HIS   ( 122-)  B      CG   ND1  CE1 109.66    4.1
 350 HIS   ( 130-)  B      CG   ND1  CE1 109.82    4.2
 563 HIS   ( 122-)  C      CG   ND1  CE1 110.13    4.5
 635 MET   ( 194-)  C      N    CA   C    99.56   -4.2
1001 HIS   ( 130-)  E      CG   ND1  CE1 109.75    4.1
1185 HIS   (  98-)  F      CG   ND1  CE1 109.71    4.1
1217 HIS   ( 130-)  F      CG   ND1  CE1 109.67    4.1
1219 HIS   ( 132-)  F      CG   ND1  CE1 109.62    4.0
1281 MET   ( 194-)  F      N    CA   C    99.07   -4.3

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.

   1 ASP   (   2-)  A
  30 ASP   (  31-)  A
  43 ASP   (  44-)  A
 109 ASP   ( 110-)  A
 143 ASP   ( 144-)  A
 168 GLU   ( 169-)  A
 216 GLU   ( 217-)  A
 217 GLU   ( 218-)  A
 248 GLU   (  28-)  B
 276 GLU   (  56-)  B
 279 GLU   (  59-)  B
 311 GLU   (  91-)  B
 364 ASP   ( 144-)  B
 389 GLU   ( 169-)  B
 422 GLU   ( 202-)  B
 436 ASP   ( 216-)  B
 443 ASP   (   2-)  C
 462 GLU   (  21-)  C
 469 GLU   (  28-)  C
 497 GLU   (  56-)  C
 500 GLU   (  59-)  C
 553 ASP   ( 112-)  C
 581 GLU   ( 140-)  C
 585 ASP   ( 144-)  C
 610 GLU   ( 169-)  C
 626 ASP   ( 185-)  C
 658 GLU   ( 217-)  C
 659 ASP   (   2-)  D
 678 GLU   (  21-)  D
 748 GLU   (  91-)  D
 801 ASP   ( 144-)  D
 842 ASP   ( 185-)  D
 856 GLU   ( 199-)  D
 899 GLU   (  28-)  E
 927 GLU   (  56-)  E
 962 GLU   (  91-)  E
 981 ASP   ( 110-)  E
 983 ASP   ( 112-)  E
1015 ASP   ( 144-)  E
1040 GLU   ( 169-)  E
1056 ASP   ( 185-)  E
1069 ARG   ( 198-)  E
1070 GLU   ( 199-)  E
1089 ASP   (   2-)  F
1107 GLU   (  20-)  F
1178 GLU   (  91-)  F
1227 GLU   ( 140-)  F
1231 ASP   ( 144-)  F
1256 GLU   ( 169-)  F

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.

1281 MET   ( 194-)  F    4.66
 389 GLU   ( 169-)  B    4.53
 339 TRP   ( 119-)  B    4.19

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 117 ASN   ( 118-)  A    4.19

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.

 987 ILE   ( 116-)  E    -2.5
 916 SER   (  45-)  E    -2.5
 486 SER   (  45-)  C    -2.5
 115 ILE   ( 116-)  A    -2.4
 352 HIS   ( 132-)  B    -2.3
 557 ILE   ( 116-)  C    -2.3
 293 THR   (  73-)  B    -2.3
 265 SER   (  45-)  B    -2.3
 871 ILE   ( 214-)  D    -2.2
 960 LYS   (  89-)  E    -2.2
 242 ASN   (  22-)  B    -2.2
 440 ILE   ( 220-)  B    -2.2
1065 MET   ( 194-)  E    -2.2
 944 THR   (  73-)  E    -2.2
 336 ILE   ( 116-)  B    -2.2
 711 ASN   (  54-)  D    -2.2
1203 ILE   ( 116-)  F    -2.1
1109 ASN   (  22-)  F    -2.1
1293 ARG   ( 206-)  F    -2.1
 578 LEU   ( 137-)  C    -2.1
 110 LYS   ( 111-)  A    -2.1
 619 GLY   ( 178-)  C    -2.1
  44 SER   (  45-)  A    -2.1
 434 ILE   ( 214-)  B    -2.1
 135 LYS   ( 136-)  A    -2.1
 686 LEU   (  29-)  D    -2.1
1049 GLY   ( 178-)  E    -2.1
1285 ARG   ( 198-)  F    -2.1
 414 MET   ( 194-)  B    -2.1
1260 LYS   ( 173-)  F    -2.1
 398 GLY   ( 178-)  B    -2.1
 514 THR   (  73-)  C    -2.1
 357 LEU   ( 137-)  B    -2.1
 177 GLY   ( 178-)  A    -2.1
 961 ILE   (  90-)  E    -2.1
  72 THR   (  73-)  A    -2.1
 498 PRO   (  57-)  C    -2.1
  53 ASN   (  54-)  A    -2.1
 773 ILE   ( 116-)  D    -2.0
 552 LYS   ( 111-)  C    -2.0
 835 GLY   ( 178-)  D    -2.0
1207 LEU   ( 120-)  F    -2.0
 509 ASN   (  68-)  C    -2.0
 702 SER   (  45-)  D    -2.0

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.

  21 ASN   (  22-)  A  Poor phi/psi
  36 TYR   (  37-)  A  omega poor
  51 LEU   (  52-)  A  omega poor
  53 ASN   (  54-)  A  Poor phi/psi
  60 PHE   (  61-)  A  omega poor
  66 ALA   (  67-)  A  Poor phi/psi
  88 LYS   (  89-)  A  Poor phi/psi
  99 ASN   ( 100-)  A  Poor phi/psi
 111 ASP   ( 112-)  A  omega poor
 184 ASP   ( 185-)  A  Poor phi/psi
 196 SER   ( 197-)  A  Poor phi/psi
 214 LEU   ( 215-)  A  omega poor
 240 GLU   (  20-)  B  Poor phi/psi
 241 GLU   (  21-)  B  Poor phi/psi
 242 ASN   (  22-)  B  Poor phi/psi, omega poor
 251 ASP   (  31-)  B  omega poor
 281 PHE   (  61-)  B  omega poor
 287 ALA   (  67-)  B  Poor phi/psi
 351 GLY   ( 131-)  B  omega poor
 405 ASP   ( 185-)  B  Poor phi/psi
 440 ILE   ( 220-)  B  omega poor
 458 ARG   (  17-)  C  Poor phi/psi
 459 MET   (  18-)  C  Poor phi/psi
 465 THR   (  24-)  C  Poor phi/psi
 473 HIS   (  32-)  C  Poor phi/psi, omega poor
And so on for a total of 59 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.030

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.

 520 SER   (  79-)  C    0.36
  12 SER   (  13-)  A    0.36
 454 SER   (  13-)  C    0.36
 299 SER   (  79-)  B    0.37
 233 SER   (  13-)  B    0.37
1291 SER   ( 204-)  F    0.38
 670 SER   (  13-)  D    0.39
1100 SER   (  13-)  F    0.40

Warning: Unusual backbone conformations

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

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

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

  22 SER   (  23-)  A      0
  32 GLN   (  33-)  A      0
  43 ASP   (  44-)  A      0
  44 SER   (  45-)  A      0
  45 ARG   (  46-)  A      0
  46 VAL   (  47-)  A      0
  56 PRO   (  57-)  A      0
  58 GLU   (  59-)  A      0
  64 ASN   (  65-)  A      0
  65 VAL   (  66-)  A      0
  66 ALA   (  67-)  A      0
  68 GLN   (  69-)  A      0
  72 THR   (  73-)  A      0
  85 ASP   (  86-)  A      0
  87 LEU   (  88-)  A      0
  88 LYS   (  89-)  A      0
  90 GLU   (  91-)  A      0
  98 THR   (  99-)  A      0
 100 CYS   ( 101-)  A      0
 112 LEU   ( 113-)  A      0
 114 LEU   ( 115-)  A      0
 129 HIS   ( 130-)  A      0
 172 LYS   ( 173-)  A      0
 178 TRP   ( 179-)  A      0
 190 GLN   ( 191-)  A      0
And so on for a total of 405 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!

 458 ARG   (  17-)  C   1.75   12

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]

  34 PRO   (  35-)  A    0.11 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].

  56 PRO   (  57-)  A   103.1 envelop C-beta (108 degrees)
 277 PRO   (  57-)  B   112.4 envelop C-beta (108 degrees)
 476 PRO   (  35-)  C   -50.9 half-chair C-beta/C-alpha (-54 degrees)
 498 PRO   (  57-)  C  -143.5 envelop C-delta (-144 degrees)
 580 PRO   ( 139-)  C   100.1 envelop C-beta (108 degrees)
 705 PRO   (  48-)  D  -114.4 envelop C-gamma (-108 degrees)
 714 PRO   (  57-)  D  -168.4 half-chair N/C-delta (-162 degrees)
 906 PRO   (  35-)  E  -116.8 envelop C-gamma (-108 degrees)
 919 PRO   (  48-)  E  -154.8 half-chair N/C-delta (-162 degrees)
 928 PRO   (  57-)  E  -119.2 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

 606 LYS   ( 165-)  C      CD  <->  639 ARG   ( 198-)  C      NH1    0.62    2.48  INTRA BF
1178 GLU   (  91-)  F      CG  <-> 1320 HOH   ( 249 )  F      O      0.61    2.19  INTRA BF
 107 MET   ( 108-)  A      SD  <->  126 TRP   ( 127-)  A      CZ3    0.50    2.90  INTRA BF
 726 GLN   (  69-)  D      CG  <-> 1318 HOH   ( 253 )  D      O      0.48    2.32  INTRA BL
 961 ILE   (  90-)  E      CD1 <->  963 HIS   (  92-)  E      O      0.44    2.36  INTRA BL
 943 HIS   (  72-)  E      NE2 <-> 1212 ASP   ( 125-)  F      OD2    0.41    2.29  INTRA BL
1031 ARG   ( 160-)  E      NH2 <-> 1212 ASP   ( 125-)  F      OD1    0.39    2.31  INTRA BL
 112 LEU   ( 113-)  A      N   <->  116 ASN   ( 117-)  A      ND2    0.38    2.47  INTRA BL
 696 TRP   (  39-)  D      NE1 <-> 1318 HOH   ( 237 )  D      O      0.36    2.34  INTRA BL
 770 LEU   ( 113-)  D      N   <->  774 ASN   ( 117-)  D      ND2    0.36    2.49  INTRA BF
 457 GLN   (  16-)  C      O   <->  459 MET   (  18-)  C      N      0.34    2.36  INTRA BF
 116 ASN   ( 117-)  A      ND2 <-> 1315 HOH   ( 229 )  A      O      0.32    2.38  INTRA BF
 128 LYS   ( 129-)  A      O   <->  131 HIS   ( 132-)  A      CE1    0.30    2.50  INTRA BF
  71 HIS   (  72-)  A      ND1 <-> 1315 HOH   ( 257 )  A      O      0.29    2.41  INTRA BL
 732 PHE   (  75-)  D      N   <-> 1310 ACT   ( 222-)  D      CH3    0.29    2.81  INTRA BL
 709 LEU   (  52-)  D      O   <-> 1098 ASN   (  11-)  F      ND2    0.27    2.43  INTRA BF
 516 PHE   (  75-)  C      N   <-> 1314 ACT   ( 222-)  C      CH3    0.27    2.83  INTRA BL
 393 LYS   ( 173-)  B      CD  <->  394 LEU   ( 174-)  B      N      0.26    2.74  INTRA BF
 726 GLN   (  69-)  D      CD  <-> 1318 HOH   ( 253 )  D      O      0.25    2.55  INTRA BL
 131 HIS   ( 132-)  A      CD2 <->  132 LEU   ( 133-)  A      N      0.25    2.75  INTRA BF
1043 GLN   ( 172-)  E      NE2 <-> 1319 HOH   ( 233 )  E      O      0.24    2.46  INTRA BF
1173 ASP   (  86-)  F      O   <-> 1176 LYS   (  89-)  F      NZ     0.24    2.46  INTRA BF
 822 LYS   ( 165-)  D      NZ  <-> 1318 HOH   ( 252 )  D      O      0.24    2.46  INTRA BL
 257 TYR   (  37-)  B      O   <->  281 PHE   (  61-)  B      N      0.23    2.47  INTRA BL
1131 ASP   (  44-)  F      CB  <-> 1313  CO   ( 230-)  F     CO      0.23    2.97  INTRA BL
And so on for a total of 207 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

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.

 266 ARG   (  46-)  B      -6.83
  45 ARG   (  46-)  A      -6.80
 284 ARG   (  64-)  B      -6.34
  32 GLN   (  33-)  A      -6.31
 474 GLN   (  33-)  C      -6.20
  63 ARG   (  64-)  A      -6.15
 253 GLN   (  33-)  B      -5.86
1133 ARG   (  46-)  F      -5.84
 904 GLN   (  33-)  E      -5.73
1120 GLN   (  33-)  F      -5.70
 703 ARG   (  46-)  D      -5.58
 917 ARG   (  46-)  E      -5.57
 690 GLN   (  33-)  D      -5.52
 487 ARG   (  46-)  C      -5.51
 971 ASN   ( 100-)  E      -5.15
 757 ASN   ( 100-)  D      -5.09
1151 ARG   (  64-)  F      -5.09

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: 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

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.

1315 HOH   ( 236 )  A      O
1319 HOH   ( 240 )  E      O
1320 HOH   ( 225 )  F      O
Metal-coordinating Histidine residue  97 fixed to   1
Metal-coordinating Histidine residue 318 fixed to   1
Metal-coordinating Histidine residue 539 fixed to   1
Metal-coordinating Histidine residue 755 fixed to   1
Metal-coordinating Histidine residue 969 fixed to   2
Metal-coordinating Histidine residue1185 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.

   5 GLN   (   6-)  A
  31 HIS   (  32-)  A
  35 HIS   (  36-)  A
 447 GLN   (   6-)  C
 473 HIS   (  32-)  C
 989 ASN   ( 118-)  E
1120 GLN   (  33-)  F
1123 HIS   (  36-)  F

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.

   4 LYS   (   5-)  A      N
   4 LYS   (   5-)  A      NZ
  13 TRP   (  14-)  A      NE1
  15 GLN   (  16-)  A      NE2
  24 TYR   (  25-)  A      OH
  25 PHE   (  26-)  A      N
  49 GLU   (  50-)  A      N
  72 THR   (  73-)  A      N
  76 CYS   (  77-)  A      N
 112 LEU   ( 113-)  A      N
 136 LEU   ( 137-)  A      N
 139 GLU   ( 140-)  A      N
 224 ILE   (   4-)  B      N
 246 PHE   (  26-)  B      N
 253 GLN   (  33-)  B      N
 269 ALA   (  49-)  B      N
 284 ARG   (  64-)  B      N
 292 HIS   (  72-)  B      N
 293 THR   (  73-)  B      N
 295 PHE   (  75-)  B      N
 312 HIS   (  92-)  B      N
 394 LEU   ( 174-)  B      N
 418 ARG   ( 198-)  B      NH1
 459 MET   (  18-)  C      N
 462 GLU   (  21-)  C      N
And so on for a total of 83 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.

 289 GLN   (  69-)  B      OE1
 296 ASN   (  76-)  B      OD1
 312 HIS   (  92-)  B      NE2
 510 GLN   (  69-)  C      OE1
 517 ASN   (  76-)  C      OD1
 716 GLU   (  59-)  D      OE1

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.

  20 GLU   (  21-)  A   H-bonding suggests Gln; but Alt-Rotamer
 139 GLU   ( 140-)  A   H-bonding suggests Gln
 251 ASP   (  31-)  B   H-bonding suggests Asn; but Alt-Rotamer
 472 ASP   (  31-)  C   H-bonding suggests Asn; but Alt-Rotamer
 581 GLU   ( 140-)  C   H-bonding suggests Gln
 688 ASP   (  31-)  D   H-bonding suggests Asn; but Alt-Rotamer
1056 ASP   ( 185-)  E   H-bonding suggests Asn; but Alt-Rotamer
1118 ASP   (  31-)  F   H-bonding suggests Asn; but Alt-Rotamer
1212 ASP   ( 125-)  F   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.358
  2nd generation packing quality :  -1.345
  Ramachandran plot appearance   :  -1.320
  chi-1/chi-2 rotamer normality  :  -4.030 (bad)
  Backbone conformation          :   0.073

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.799
  Bond angles                    :   0.881
  Omega angle restraints         :   1.136
  Side chain planarity           :   0.842
  Improper dihedral distribution :   0.936
  B-factor distribution          :   0.441
  Inside/Outside distribution    :   1.017

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.4
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.799
  Bond angles                    :   0.881
  Omega angle restraints         :   1.136
  Side chain planarity           :   0.842
  Improper dihedral distribution :   0.936
  B-factor distribution          :   0.441
  Inside/Outside distribution    :   1.017
==============

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.