WHAT IF Check report

This file was created 2012-01-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1w1x.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 106.993  B   =  73.464  C    = 107.413
    Alpha=  90.000  Beta=  90.380  Gamma=  90.000

Dimensions of a reduced cell

    A    =  73.464  B   = 106.993  C    = 107.413
    Alpha=  90.380  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 107.413  B   = 106.993  C    =  73.464
    Alpha=  90.000  Beta=  90.000  Gamma=  89.620

Transformation to conventional cell

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

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 1 21 1

Bravais type of conventional cell is: P

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 : 0.554
CA-only RMS fit for the two chains : 0.190

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 : 0.451
CA-only RMS fit for the two chains : 0.191

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 : 0.457
CA-only RMS fit for the two chains : 0.182

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 : 0.490
CA-only RMS fit for the two chains : 0.175

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: 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 : 0.467
CA-only RMS fit for the two chains : 0.154

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: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

1570 SIA   (1477-)  A  -
1571 SIA   (1478-)  A  -
1573 BMA   (1480-)  A  -
1574 MAN   (1481-)  A  -
1575 MAN   (1482-)  A  -
1576 MAN   (1483-)  A  -
1578 SIA   (2477-)  B  -
1579 SIA   (2478-)  B  -
1581 BMA   (2480-)  B  -
1582 MAN   (2481-)  B  -
1583 MAN   (2482-)  B  -
1584 MAN   (2483-)  B  -
1586 SIA   (3477-)  C  -
1587 SIA   (3478-)  C  -
1589 BMA   (3480-)  C  -
1590 MAN   (3481-)  C  -
1591 MAN   (3482-)  C  -
1592 MAN   (3483-)  C  -
1594 SIA   (4477-)  D  -
1597 BMA   (4480-)  C  -
1598 SIA   (4478-)  D  -
1599 MAN   (3484-)  C  -
1600 PEG   (3476-)  C  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

1287 ASN   (3207-)  D  -   ND2 1563 NAG   (2487-)  B  -   C1

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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.

1560 NAG   (1488-)  A  -   O4  bound to 1559 NAG   (1486-)  A  -   C1
1566 NAG   (3487-)  C  -   O4  bound to 1567 NAG   (4481-)  C  -   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: 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: Arginine nomenclature problem

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

  37 ARG   ( 124-)  A
 109 ARG   ( 196-)  A
 130 ARG   ( 217-)  A
 426 ARG   (1124-)  B
 498 ARG   (1196-)  B
 609 ARG   (1307-)  B
 815 ARG   (2124-)  C
 887 ARG   (2196-)  C
 908 ARG   (2217-)  C
1204 ARG   (3124-)  D
1216 ARG   (3136-)  D
1276 ARG   (3196-)  D

Warning: Tyrosine convention problem

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

  89 TYR   ( 176-)  A
 127 TYR   ( 214-)  A
 387 TYR   ( 474-)  A
 478 TYR   (1176-)  B
 516 TYR   (1214-)  B
 733 TYR   (1431-)  B
 776 TYR   (1474-)  B
 867 TYR   (2176-)  C
 905 TYR   (2214-)  C
1072 TYR   (2381-)  C
1122 TYR   (2431-)  C
1165 TYR   (2474-)  C
1256 TYR   (3176-)  D
1294 TYR   (3214-)  D
1368 TYR   (3288-)  D
1554 TYR   (3474-)  D

Warning: Phenylalanine convention problem

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

   3 PHE   (  90-)  A
  74 PHE   ( 161-)  A
 388 PHE   ( 475-)  A
 392 PHE   (1090-)  B
 463 PHE   (1161-)  B
 566 PHE   (1264-)  B
 732 PHE   (1430-)  B
 777 PHE   (1475-)  B
 781 PHE   (2090-)  C
 852 PHE   (2161-)  C
 955 PHE   (2264-)  C
1121 PHE   (2430-)  C
1166 PHE   (2475-)  C
1170 PHE   (3090-)  D
1241 PHE   (3161-)  D
1344 PHE   (3264-)  D
1510 PHE   (3430-)  D

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.

  30 ASP   ( 117-)  A
  44 ASP   ( 131-)  A
 163 ASP   ( 250-)  A
 213 ASP   ( 300-)  A
 226 ASP   ( 313-)  A
 250 ASP   ( 337-)  A
 257 ASP   ( 344-)  A
 276 ASP   ( 363-)  A
 419 ASP   (1117-)  B
 433 ASP   (1131-)  B
 552 ASP   (1250-)  B
 602 ASP   (1300-)  B
 615 ASP   (1313-)  B
 639 ASP   (1337-)  B
 646 ASP   (1344-)  B
 665 ASP   (1363-)  B
 808 ASP   (2117-)  C
 822 ASP   (2131-)  C
 941 ASP   (2250-)  C
 991 ASP   (2300-)  C
1004 ASP   (2313-)  C
1028 ASP   (2337-)  C
1035 ASP   (2344-)  C
1054 ASP   (2363-)  C
1197 ASP   (3117-)  D
1211 ASP   (3131-)  D
1330 ASP   (3250-)  D
1380 ASP   (3300-)  D
1393 ASP   (3313-)  D
1417 ASP   (3337-)  D
1424 ASP   (3344-)  D
1443 ASP   (3363-)  D

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.

  12 GLU   (  99-)  A
  29 GLU   ( 116-)  A
  38 GLU   ( 125-)  A
 134 GLU   ( 221-)  A
 147 GLU   ( 234-)  A
 196 GLU   ( 283-)  A
 278 GLU   ( 365-)  A
 303 GLU   ( 390-)  A
 346 GLU   ( 433-)  A
 354 GLU   ( 441-)  A
 384 GLU   ( 471-)  A
 401 GLU   (1099-)  B
 418 GLU   (1116-)  B
 427 GLU   (1125-)  B
 523 GLU   (1221-)  B
 536 GLU   (1234-)  B
 667 GLU   (1365-)  B
 692 GLU   (1390-)  B
 726 GLU   (1424-)  B
 735 GLU   (1433-)  B
 743 GLU   (1441-)  B
 773 GLU   (1471-)  B
 790 GLU   (2099-)  C
 807 GLU   (2116-)  C
 816 GLU   (2125-)  C
 912 GLU   (2221-)  C
 925 GLU   (2234-)  C
1006 GLU   (2315-)  C
1081 GLU   (2390-)  C
1124 GLU   (2433-)  C
1132 GLU   (2441-)  C
1162 GLU   (2471-)  C
1179 GLU   (3099-)  D
1196 GLU   (3116-)  D
1205 GLU   (3125-)  D
1301 GLU   (3221-)  D
1314 GLU   (3234-)  D
1363 GLU   (3283-)  D
1395 GLU   (3315-)  D
1470 GLU   (3390-)  D
1513 GLU   (3433-)  D
1521 GLU   (3441-)  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.

  90 ASN   ( 177-)  A      CB   CG    1.62    4.0
 103 CYS   ( 190-)  A      CA   C     1.61    4.1
 133 THR   ( 220-)  A      CA   CB    1.62    4.4
 265 PRO   ( 352-)  A      CG   CD    1.64    4.1
 319 ASN   ( 406-)  A      CG   OD1   1.31    4.1
 485 ILE   (1183-)  B      CB   CG2   1.70    4.9
 502 CYS   (1200-)  B      N    CA    1.54    4.1
 578 ALA   (1276-)  B      N    CA    1.54    4.2
 588 SER   (1286-)  B      CB   OG    1.50    4.1
 713 GLY   (1411-)  B      CA   C     1.58    4.2
 730 PRO   (1428-)  B      CB   CG    1.73    4.7
 777 PHE   (1475-)  B      CD1  CE1   1.51    4.4
 799 LYS   (2108-)  C      CB   CG    1.65    4.5
 805 ILE   (2114-)  C      CA   CB    1.64    5.7
 870 ARG   (2179-)  C      NE   CZ    1.39    4.1
 926 SER   (2235-)  C      CA   C     1.62    4.5
1008 MET   (2317-)  C      SD   CE    2.08    4.8
1024 SER   (2333-)  C      CA   CB    1.44   -4.5
1190 ASN   (3110-)  D      C    O     1.32    4.5
1194 ILE   (3114-)  D      CA   CB    1.63    5.0
1233 GLY   (3153-)  D      CA   C     1.58    4.6
1242 ARG   (3162-)  D      CB   CG    1.66    4.8
1309 ILE   (3229-)  D      CA   CB    1.63    4.8
1348 LYS   (3268-)  D      CE   NZ    1.65    5.3
1552 ILE   (3472-)  D      CA   CB    1.62    4.4
1555 PHE   (3475-)  D      CD1  CE1   1.53    5.1

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

 |  0.995460 -0.000095 -0.001200|
 | -0.000095  0.988593 -0.000121|
 | -0.001200 -0.000121  0.995649|
Proposed new scale matrix

 |  0.009389  0.000000  0.000075|
 |  0.000001  0.013769  0.000002|
 |  0.000011  0.000001  0.009351|
With corresponding cell

    A    = 106.512  B   =  72.627  C    = 106.948
    Alpha=  90.014  Beta=  90.524  Gamma=  90.006

The CRYST1 cell dimensions

    A    = 106.993  B   =  73.464  C    = 107.413
    Alpha=  90.000  Beta=  90.380  Gamma=  90.000

Variance: 2658.371
(Under-)estimated Z-score: 37.999

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.

  32 HIS   ( 119-)  A      CG   ND1  CE1 110.11    4.5
  39 PRO   ( 126-)  A      C    CA   CB  102.37   -4.1
  41 LEU   ( 128-)  A      CA   CB   CG  131.59    4.4
 186 GLU   ( 273-)  A      C    CA   CB  101.94   -4.3
 246 SER   ( 333-)  A     -CA  -C    N   106.77   -4.7
 246 SER   ( 333-)  A     -C    N    CA  132.90    6.2
 246 SER   ( 333-)  A      N    CA   C    95.74   -5.5
 246 SER   ( 333-)  A      C    CA   CB  120.55    5.5
 267 PRO   ( 354-)  A      CA   C    O   113.68   -4.2
 373 ARG   ( 460-)  A      CG   CD   NE  117.39    4.1
 380 HIS   ( 467-)  A      CG   ND1  CE1 109.72    4.1
 421 HIS   (1119-)  B      CG   ND1  CE1 109.98    4.4
 425 THR   (1123-)  B      CG2  CB   OG1 101.22   -4.0
 430 LEU   (1128-)  B      CA   CB   CG  131.53    4.4
 583 HIS   (1281-)  B      CG   ND1  CE1 109.60    4.0
 635 SER   (1333-)  B     -O   -C    N   131.70    5.4
 635 SER   (1333-)  B     -CA  -C    N   105.16   -5.5
 635 SER   (1333-)  B     -C    N    CA  134.87    7.3
 635 SER   (1333-)  B      N    CA   C    94.56   -5.9
 635 SER   (1333-)  B      C    CA   CB  122.54    6.5
 769 HIS   (1467-)  B      CG   ND1  CE1 109.94    4.3
 810 HIS   (2119-)  C      CG   ND1  CE1 110.26    4.7
 819 LEU   (2128-)  C      CA   CB   CG  131.30    4.3
 847 HIS   (2156-)  C     -C    N    CA  128.98    4.0
 931 HIS   (2240-)  C      CG   ND1  CE1 109.66    4.1
1010 HIS   (2319-)  C      CG   ND1  CE1 109.69    4.1
1024 SER   (2333-)  C     -O   -C    N   130.45    4.7
1024 SER   (2333-)  C     -CA  -C    N   106.49   -4.9
1024 SER   (2333-)  C     -C    N    CA  133.81    6.7
1024 SER   (2333-)  C      N    CA   C    95.65   -5.6
1024 SER   (2333-)  C      C    CA   CB  118.90    4.6
1184 HIS   (3104-)  D      CG   ND1  CE1 109.79    4.2
1199 HIS   (3119-)  D      CG   ND1  CE1 110.40    4.8
1230 HIS   (3150-)  D      CG   ND1  CE1 109.73    4.1
1236 HIS   (3156-)  D      CG   ND1  CE1 109.66    4.1
1287 ASN   (3207-)  D      N    CA   CB  103.70   -4.0
1399 HIS   (3319-)  D      CG   ND1  CE1 109.78    4.2
1413 SER   (3333-)  D     -CA  -C    N   107.56   -4.3
1413 SER   (3333-)  D     -C    N    CA  134.26    7.0
1413 SER   (3333-)  D      N    CA   C    91.81   -6.9
1413 SER   (3333-)  D      C    CA   CB  120.18    5.3
1420 ASN   (3340-)  D      C    CA   CB  101.10   -4.7
1424 ASP   (3344-)  D      CA   CB   CG  108.59   -4.0
1553 ILE   (3473-)  D      CG2  CB   CG1  98.62   -4.0

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.

  12 GLU   (  99-)  A
  29 GLU   ( 116-)  A
  30 ASP   ( 117-)  A
  37 ARG   ( 124-)  A
  38 GLU   ( 125-)  A
  44 ASP   ( 131-)  A
 109 ARG   ( 196-)  A
 130 ARG   ( 217-)  A
 134 GLU   ( 221-)  A
 147 GLU   ( 234-)  A
 163 ASP   ( 250-)  A
 196 GLU   ( 283-)  A
 213 ASP   ( 300-)  A
 226 ASP   ( 313-)  A
 250 ASP   ( 337-)  A
 257 ASP   ( 344-)  A
 276 ASP   ( 363-)  A
 278 GLU   ( 365-)  A
 303 GLU   ( 390-)  A
 346 GLU   ( 433-)  A
 354 GLU   ( 441-)  A
 384 GLU   ( 471-)  A
 401 GLU   (1099-)  B
 418 GLU   (1116-)  B
 419 ASP   (1117-)  B
And so on for a total of 86 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  41 LEU   ( 128-)  A      CG     6.1   -22.25   -33.01
1466 VAL   (3386-)  D      CB     7.7   -22.89   -32.96
The average deviation= 1.486

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.

1413 SER   (3333-)  D    7.55
 635 SER   (1333-)  B    6.50
1024 SER   (2333-)  C    6.09
 246 SER   ( 333-)  A    6.05
 898 ASN   (2207-)  C    4.72
 100 SER   ( 187-)  A    4.34
 975 GLU   (2284-)  C    4.19
 489 SER   (1187-)  B    4.00

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.

1091 ASN   (2400-)  C    4.99
1424 ASP   (3344-)  D    4.35
 313 ASN   ( 400-)  A    4.14
 690 ASN   (1388-)  B    4.06

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.

 265 PRO   ( 352-)  A    -3.0
1043 PRO   (2352-)  C    -3.0
1432 PRO   (3352-)  D    -2.9
 654 PRO   (1352-)  B    -2.8
 145 THR   ( 232-)  A    -2.8
1024 SER   (2333-)  C    -2.7
 635 SER   (1333-)  B    -2.7
 534 THR   (1232-)  B    -2.7
1413 SER   (3333-)  D    -2.7
1312 THR   (3232-)  D    -2.7
 373 ARG   ( 460-)  A    -2.7
 246 SER   ( 333-)  A    -2.7
 923 THR   (2232-)  C    -2.6
 835 THR   (2144-)  C    -2.5
 815 ARG   (2124-)  C    -2.5
  37 ARG   ( 124-)  A    -2.5
  57 THR   ( 144-)  A    -2.5
1204 ARG   (3124-)  D    -2.5
 426 ARG   (1124-)  B    -2.5
1224 THR   (3144-)  D    -2.5
1114 LYS   (2423-)  C    -2.5
 741 PRO   (1439-)  B    -2.4
 385 ILE   ( 472-)  A    -2.4
 446 THR   (1144-)  B    -2.4
 879 THR   (2188-)  C    -2.4
And so on for a total of 78 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.

   4 LEU   (  91-)  A  omega poor
  23 ASN   ( 110-)  A  omega poor
  37 ARG   ( 124-)  A  Poor phi/psi
  52 ALA   ( 139-)  A  Poor phi/psi
 142 ILE   ( 229-)  A  Poor phi/psi
 145 THR   ( 232-)  A  Poor phi/psi, omega poor
 147 GLU   ( 234-)  A  Poor phi/psi
 196 GLU   ( 283-)  A  omega poor
 210 ILE   ( 297-)  A  omega poor
 230 MET   ( 317-)  A  Poor phi/psi
 235 LYS   ( 322-)  A  Poor phi/psi
 238 CYS   ( 325-)  A  omega poor
 245 THR   ( 332-)  A  omega poor
 246 SER   ( 333-)  A  Poor phi/psi
 264 SER   ( 351-)  A  PRO omega poor
 279 ASN   ( 366-)  A  Poor phi/psi
 291 ARG   ( 378-)  A  Poor phi/psi
 301 ASN   ( 388-)  A  Poor phi/psi
 304 THR   ( 391-)  A  Poor phi/psi
 323 SER   ( 410-)  A  Poor phi/psi
 351 ARG   ( 438-)  A  PRO omega poor
 361 SER   ( 448-)  A  Poor phi/psi
 423 LEU   (1121-)  B  omega poor
 427 GLU   (1125-)  B  Poor phi/psi
 441 ALA   (1139-)  B  Poor phi/psi
And so on for a total of 90 lines.

Warning: Unusual backbone conformations

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

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

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

   6 LEU   (  93-)  A      0
   7 THR   (  94-)  A      0
  14 ASN   ( 101-)  A      0
  20 SER   ( 107-)  A      0
  22 ASP   ( 109-)  A      0
  30 ASP   ( 117-)  A      0
  31 ALA   ( 118-)  A      0
  37 ARG   ( 124-)  A      0
  38 GLU   ( 125-)  A      0
  39 PRO   ( 126-)  A      0
  40 TYR   ( 127-)  A      0
  46 GLN   ( 133-)  A      0
  48 CYS   ( 135-)  A      0
  55 GLN   ( 142-)  A      0
  63 HIS   ( 150-)  A      0
  65 ASN   ( 152-)  A      0
  67 THR   ( 154-)  A      0
  68 ILE   ( 155-)  A      0
  69 HIS   ( 156-)  A      0
  71 ARG   ( 158-)  A      0
  72 SER   ( 159-)  A      0
  80 TRP   ( 167-)  A      0
  82 MET   ( 169-)  A      0
  94 GLU   ( 181-)  A      0
  95 CYS   ( 182-)  A      0
And so on for a total of 870 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!

 263 GLY   ( 350-)  A   1.87   11
1041 GLY   (2350-)  C   1.86   19

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]

 648 PRO   (1346-)  B    0.47 HIGH
 895 PRO   (2204-)  C    0.49 HIGH
1394 PRO   (3314-)  D    0.20 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].

 265 PRO   ( 352-)  A   -45.1 half-chair C-beta/C-alpha (-54 degrees)
 310 PRO   ( 397-)  A    52.6 half-chair C-delta/C-gamma (54 degrees)
 462 PRO   (1160-)  B    52.3 half-chair C-delta/C-gamma (54 degrees)
 654 PRO   (1352-)  B   -46.9 half-chair C-beta/C-alpha (-54 degrees)
 699 PRO   (1397-)  B    47.0 half-chair C-delta/C-gamma (54 degrees)
 851 PRO   (2160-)  C    52.2 half-chair C-delta/C-gamma (54 degrees)
1043 PRO   (2352-)  C   -63.5 envelop C-beta (-72 degrees)
1432 PRO   (3352-)  D   -45.9 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

 208 LYS   ( 295-)  A      NZ   <->  1601 HOH   (2206 )  A      O    2.16    0.54  INTRA
 208 LYS   ( 295-)  A      CE   <->  1601 HOH   (2206 )  A      O    1.77    1.03  INTRA
   5 ASN   (  92-)  A      ND2  <->  1557 NAG   (1484-)  A      C1   1.24    1.86  INTRA
  65 ASN   ( 152-)  A      ND2  <->  1558 NAG   (1485-)  A      C1   1.24    1.86  INTRA
1232 ASN   (3152-)  D      ND2  <->  1568 NAG   (4482-)  D      C1   1.22    1.88  INTRA
 454 ASN   (1152-)  B      ND2  <->  1561 NAG   (2484-)  B      C1   1.08    2.02  INTRA
 898 ASN   (2207-)  C      ND2  <->  1566 NAG   (3487-)  C      C1   1.06    2.04  INTRA BF
1589 BMA   (3480-)  C      O6   <->  1591 MAN   (3482-)  C      C1   1.02    1.78  INTRA BF
1582 MAN   (2481-)  B      O6   <->  1583 MAN   (2482-)  B      C1   1.02    1.78  INTRA BF
 843 ASN   (2152-)  C      ND2  <->  1565 NAG   (3486-)  C      C1   1.02    2.08  INTRA
1574 MAN   (1481-)  A      O6   <->  1575 MAN   (1482-)  A      C1   0.95    1.85  INTRA BF
 509 ASN   (1207-)  B      ND2  <->  1560 NAG   (1488-)  A      C2   0.93    2.17  INTRA BF
1573 BMA   (1480-)  A      O6   <->  1574 MAN   (1481-)  A      C1   0.92    1.88  INTRA BF
1562 NAG   (2485-)  B      O4   <->  1581 BMA   (2480-)  B      C1   0.83    1.97  INTRA BF
1564 NAG   (3485-)  C      O4   <->  1589 BMA   (3480-)  C      C1   0.81    1.99  INTRA BF
1591 MAN   (3482-)  C      O6   <->  1592 MAN   (3483-)  C      C1   0.71    2.09  INTRA BF
1581 BMA   (2480-)  B      O6   <->  1582 MAN   (2481-)  B      C1   0.69    2.11  INTRA BF
 509 ASN   (1207-)  B      ND2  <->  1560 NAG   (1488-)  A      C1   0.67    2.43  INTRA BF
 208 LYS   ( 295-)  A      CD   <->  1601 HOH   (2206 )  A      O    0.67    2.13  INTRA
1559 NAG   (1486-)  A      O4   <->  1573 BMA   (1480-)  A      C1   0.66    2.14  INTRA BF
1562 NAG   (2485-)  B      C1   <->  1563 NAG   (2487-)  B      O4   0.63    1.97  INTRA
1567 NAG   (4481-)  C      O4   <->  1597 BMA   (4480-)  C      C1   0.62    2.18  INTRA
1574 MAN   (1481-)  A      O3   <->  1576 MAN   (1483-)  A      C1   0.62    2.18  INTRA
1591 MAN   (3482-)  C      C3   <->  1599 MAN   (3484-)  C      C1   0.60    2.60  INTRA
1591 MAN   (3482-)  C      O3   <->  1599 MAN   (3484-)  C      C1   0.59    2.21  INTRA
And so on for a total of 264 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.

 947 ARG   (2256-)  C      -7.54
 373 ARG   ( 460-)  A      -7.44
1336 ARG   (3256-)  D      -7.27
 558 ARG   (1256-)  B      -7.26
 169 ARG   ( 256-)  A      -7.15
1151 ARG   (2460-)  C      -6.89
 762 ARG   (1460-)  B      -6.70
  46 GLN   ( 133-)  A      -6.60
 824 GLN   (2133-)  C      -6.56
1540 ARG   (3460-)  D      -6.52
 435 GLN   (1133-)  B      -6.52
1213 GLN   (3133-)  D      -6.41
  71 ARG   ( 158-)  A      -6.06
 849 ARG   (2158-)  C      -5.86
1238 ARG   (3158-)  D      -5.83
 460 ARG   (1158-)  B      -5.82
 320 GLN   ( 407-)  A      -5.40
1085 GLN   (2394-)  C      -5.40
 618 MET   (1316-)  B      -5.34
 696 GLN   (1394-)  B      -5.34
 335 ASN   ( 422-)  A      -5.33
 724 ASN   (1422-)  B      -5.33
1474 GLN   (3394-)  D      -5.29
1502 ASN   (3422-)  D      -5.25
1396 MET   (3316-)  D      -5.25
 971 GLN   (2280-)  C      -5.24
 307 GLN   ( 394-)  A      -5.21
 709 GLN   (1407-)  B      -5.21
 898 ASN   (2207-)  C      -5.19
 193 GLN   ( 280-)  A      -5.14
1136 LEU   (2445-)  C      -5.13
 897 ASN   (2206-)  C      -5.12
1098 GLN   (2407-)  C      -5.12
 747 LEU   (1445-)  B      -5.11
1360 GLN   (3280-)  D      -5.08
1113 ASN   (2422-)  C      -5.07
1007 MET   (2316-)  C      -5.06
1525 LEU   (3445-)  D      -5.02

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.

 336 LYS   ( 423-)  A   -3.11
1503 LYS   (3423-)  D   -3.03
1114 LYS   (2423-)  C   -2.92
   5 ASN   (  92-)  A   -2.87
 809 ALA   (2118-)  C   -2.72
1198 ALA   (3118-)  D   -2.64
  31 ALA   ( 118-)  A   -2.63
1092 GLN   (2401-)  C   -2.57
1502 ASN   (3422-)  D   -2.56
 314 GLN   ( 401-)  A   -2.55
 703 GLN   (1401-)  B   -2.54
 313 ASN   ( 400-)  A   -2.53
1481 GLN   (3401-)  D   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 773 GLU   (1471-)  B     -  776 TYR   (1474-)  B        -1.54
1111 TRP   (2420-)  C     - 1114 LYS   (2423-)  C        -1.99
1500 TRP   (3420-)  D     - 1503 LYS   (3423-)  D        -2.05

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1603 HOH   (3043 )  C      O     29.30  -25.85  118.36

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.

1601 HOH   (2001 )  A      O
1601 HOH   (2146 )  A      O
1601 HOH   (2376 )  A      O
1602 HOH   (2171 )  B      O
1602 HOH   (2344 )  B      O
1602 HOH   (2373 )  B      O
1603 HOH   (3175 )  C      O
1603 HOH   (3182 )  C      O
1604 HOH   (2033 )  D      O
1604 HOH   (2402 )  D      O
Bound group on Asn; dont flip 1287 ASN  (3207-) D
Bound to: 1563 NAG  (2487-) B

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.

  32 HIS   ( 119-)  A
 141 ASN   ( 228-)  A
 146 GLN   ( 233-)  A
 153 HIS   ( 240-)  A
 183 GLN   ( 270-)  A
 194 HIS   ( 281-)  A
 313 ASN   ( 400-)  A
 321 ASN   ( 408-)  A
 340 ASN   ( 427-)  A
 362 ASN   ( 449-)  A
 444 GLN   (1142-)  B
 493 HIS   (1191-)  B
 508 ASN   (1206-)  B
 535 GLN   (1233-)  B
 542 HIS   (1240-)  B
 572 GLN   (1270-)  B
 583 HIS   (1281-)  B
 644 ASN   (1342-)  B
 708 ASN   (1406-)  B
 724 ASN   (1422-)  B
 729 ASN   (1427-)  B
 751 ASN   (1449-)  B
 810 HIS   (2119-)  C
 841 HIS   (2150-)  C
 897 ASN   (2206-)  C
 924 GLN   (2233-)  C
 961 GLN   (2270-)  C
 972 HIS   (2281-)  C
1097 ASN   (2406-)  C
1098 GLN   (2407-)  C
1099 ASN   (2408-)  C
1118 ASN   (2427-)  C
1140 ASN   (2449-)  C
1230 HIS   (3150-)  D
1308 ASN   (3228-)  D
1313 GLN   (3233-)  D
1361 HIS   (3281-)  D
1422 ASN   (3342-)  D
1480 ASN   (3400-)  D
1502 ASN   (3422-)  D
1507 ASN   (3427-)  D
1529 ASN   (3449-)  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.

  16 TRP   ( 103-)  A      NE1
  37 ARG   ( 124-)  A      NH2
  41 LEU   ( 128-)  A      N
  57 THR   ( 144-)  A      N
  61 GLY   ( 148-)  A      N
  63 HIS   ( 150-)  A      NE2
  72 SER   ( 159-)  A      N
  89 TYR   ( 176-)  A      OH
  91 THR   ( 178-)  A      N
 104 HIS   ( 191-)  A      ND1
 106 GLY   ( 193-)  A      N
 116 GLY   ( 203-)  A      N
 148 SER   ( 235-)  A      N
 168 ASN   ( 255-)  A      N
 184 LYS   ( 271-)  A      NZ
 194 HIS   ( 281-)  A      N
 217 GLY   ( 304-)  A      N
 240 LYS   ( 327-)  A      N
 255 ASN   ( 342-)  A      ND2
 257 ASP   ( 344-)  A      N
 258 ALA   ( 345-)  A      N
 268 GLY   ( 355-)  A      N
 270 LYS   ( 357-)  A      N
 292 SER   ( 379-)  A      OG
 312 SER   ( 399-)  A      N
And so on for a total of 120 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.

 134 GLU   ( 221-)  A      OE2
 585 GLU   (1283-)  B      OE2
 795 HIS   (2104-)  C      NE2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1572  CA   (1479-)  A     0.59   0.81 Is perhaps NA *2
1580  CA   (2479-)  B     0.55   0.76 Is perhaps NA *2
1588  CA   (3479-)  C     0.51   0.72 Is perhaps NA *2
1595  CA   (4479-)  D     0.57   0.79 Is perhaps NA *2

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.

1601 HOH   (2021 )  A      O  0.93  K  4 NCS 3/3
1601 HOH   (2028 )  A      O  1.00  K  4 NCS 3/3
1601 HOH   (2091 )  A      O  0.99  K  4 ION-B NCS 1/1
1601 HOH   (2258 )  A      O  0.78 NA  4 *2 Ion-B NCS 2/2
1601 HOH   (2279 )  A      O  1.04  K  4 NCS 1/1
1601 HOH   (2309 )  A      O  0.86  K  4 Ion-B NCS 1/1
1602 HOH   (2085 )  B      O  0.87  K  5 Ion-B NCS 2/2
1602 HOH   (2329 )  B      O  0.81 NA  4 *2 NCS 3/3
1603 HOH   (3032 )  C      O  0.92  K  4 NCS 3/3
1603 HOH   (3042 )  C      O  1.09  K  4 Ion-B NCS 3/3
1604 HOH   (2061 )  D      O  0.95  K  4 NCS 3/3
1604 HOH   (2079 )  D      O  1.13  K  5 Ion-B NCS 1/1
1604 HOH   (2177 )  D      O  0.92  K  5 NCS 3/3
1604 HOH   (2312 )  D      O  0.89  K  4 NCS 2/2

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.

 105 ASP   ( 192-)  A   H-bonding suggests Asn; but Alt-Rotamer
 163 ASP   ( 250-)  A   H-bonding suggests Asn
 411 ASP   (1109-)  B   H-bonding suggests Asn; but Alt-Rotamer
 494 ASP   (1192-)  B   H-bonding suggests Asn; but Alt-Rotamer
 536 GLU   (1234-)  B   H-bonding suggests Gln
 552 ASP   (1250-)  B   H-bonding suggests Asn
 575 GLU   (1273-)  B   H-bonding suggests Gln; but Alt-Rotamer
 678 ASP   (1376-)  B   H-bonding suggests Asn; but Alt-Rotamer
 883 ASP   (2192-)  C   H-bonding suggests Asn; but Alt-Rotamer
 941 ASP   (2250-)  C   H-bonding suggests Asn; but Alt-Rotamer
 964 GLU   (2273-)  C   H-bonding suggests Gln
1272 ASP   (3192-)  D   H-bonding suggests Asn; but Alt-Rotamer
1330 ASP   (3250-)  D   H-bonding suggests Asn
1353 GLU   (3273-)  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 :  -1.006
  2nd generation packing quality :  -2.427
  Ramachandran plot appearance   :  -1.892
  chi-1/chi-2 rotamer normality  :  -2.465
  Backbone conformation          :  -1.194

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.150
  Bond angles                    :   0.987
  Omega angle restraints         :   1.165
  Side chain planarity           :   1.313
  Improper dihedral distribution :   1.237
  B-factor distribution          :   0.778
  Inside/Outside distribution    :   1.014

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.150
  Bond angles                    :   0.987
  Omega angle restraints         :   1.165
  Side chain planarity           :   1.313
  Improper dihedral distribution :   1.237
  B-factor distribution          :   0.778
  Inside/Outside distribution    :   1.014
==============

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Quality Control
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