WHAT IF Check report

This file was created 2011-12-13 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 pdb3a12.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.404
CA-only RMS fit for the two chains : 0.231

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 : 0.414
CA-only RMS fit for the two chains : 0.176

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 : 0.417
CA-only RMS fit for the two chains : 0.226

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 : 9.114
CA-only RMS fit for the two chains : 9.083

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 G

All-atom RMS fit for the two chains : 0.400
CA-only RMS fit for the two chains : 0.200

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 G

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.

4368 CAP   ( 446-)  A  -
4370 CAP   ( 446-)  B  -
4372 CAP   ( 446-)  C  -
4374 CAP   ( 446-)  D  -
4376 CAP   ( 446-)  E  -
4378 CAP   ( 446-)  F  -
4380 CAP   ( 446-)  G  -
4382 CAP   ( 446-)  H  -
4384 CAP   ( 446-)  I  -
4386 CAP   ( 446-)  J  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

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'.

   1 ILE   (   8-)  A      CG1
   1 ILE   (   8-)  A      CG2
   1 ILE   (   8-)  A      CD1
   3 ASP   (  10-)  A      CG
   3 ASP   (  10-)  A      OD1
   3 ASP   (  10-)  A      OD2
  11 GLU   (  18-)  A      CG
  11 GLU   (  18-)  A      CD
  11 GLU   (  18-)  A      OE1
  11 GLU   (  18-)  A      OE2
  50 THR   (  57-)  A      OG1
  50 THR   (  57-)  A      CG2
  51 LEU   (  58-)  A      CG
  51 LEU   (  58-)  A      CD1
  51 LEU   (  58-)  A      CD2
  52 TYR   (  59-)  A      CG
  52 TYR   (  59-)  A      CD1
  52 TYR   (  59-)  A      CD2
  52 TYR   (  59-)  A      CE1
  52 TYR   (  59-)  A      CE2
  52 TYR   (  59-)  A      CZ
  52 TYR   (  59-)  A      OH
  58 GLU   (  65-)  A      CG
  58 GLU   (  65-)  A      CD
  58 GLU   (  65-)  A      OE1
And so on for a total of 420 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: 0

Crystal temperature (K) : 95.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

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.

 115 ARG   ( 122-)  A
 497 ARG   (  66-)  B
 553 ARG   ( 122-)  B
 696 ARG   ( 265-)  B
 935 ARG   (  66-)  C
1371 ARG   (  66-)  D
1427 ARG   ( 122-)  D
1570 ARG   ( 265-)  D
1738 ARG   ( 433-)  D
1860 ARG   ( 117-)  E
2008 ARG   ( 265-)  E
2081 ARG   ( 338-)  E
2152 ARG   ( 409-)  E
2242 ARG   (  66-)  F
2609 ARG   ( 433-)  F
2729 ARG   ( 117-)  G
2734 ARG   ( 122-)  G
2877 ARG   ( 265-)  G
3607 ARG   ( 122-)  I
3918 ARG   ( 433-)  I
3988 ARG   (  66-)  J
4187 ARG   ( 265-)  J

Warning: Tyrosine convention problem

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

   5 TYR   (  12-)  A
  55 TYR   (  62-)  A
  68 TYR   (  75-)  A
  84 TYR   (  91-)  A
 443 TYR   (  12-)  B
 468 TYR   (  37-)  B
 493 TYR   (  62-)  B
 506 TYR   (  75-)  B
 522 TYR   (  91-)  B
 881 TYR   (  12-)  C
 928 TYR   (  59-)  C
 944 TYR   (  75-)  C
 960 TYR   (  91-)  C
1317 TYR   (  12-)  D
1364 TYR   (  59-)  D
1367 TYR   (  62-)  D
1396 TYR   (  91-)  D
1504 TYR   ( 199-)  D
1755 TYR   (  12-)  E
1780 TYR   (  37-)  E
1805 TYR   (  62-)  E
1818 TYR   (  75-)  E
1834 TYR   (  91-)  E
2189 TYR   (  12-)  F
2238 TYR   (  62-)  F
2251 TYR   (  75-)  F
2267 TYR   (  91-)  F
2344 TYR   ( 168-)  F
2624 TYR   (  12-)  G
2649 TYR   (  37-)  G
2671 TYR   (  59-)  G
2674 TYR   (  62-)  G
2703 TYR   (  91-)  G
2954 TYR   ( 342-)  G
3036 TYR   ( 424-)  G
3061 TYR   (  12-)  H
3108 TYR   (  59-)  H
3111 TYR   (  62-)  H
3140 TYR   (  91-)  H
3248 TYR   ( 199-)  H
3547 TYR   (  62-)  I
3560 TYR   (  75-)  I
3576 TYR   (  91-)  I
3933 TYR   (  11-)  J
3934 TYR   (  12-)  J
3984 TYR   (  62-)  J
4013 TYR   (  91-)  J

Warning: Phenylalanine convention problem

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

  70 PHE   (  77-)  A
 134 PHE   ( 141-)  A
 195 PHE   ( 202-)  A
 508 PHE   (  77-)  B
 572 PHE   ( 141-)  B
 633 PHE   ( 202-)  B
 946 PHE   (  77-)  C
1010 PHE   ( 141-)  C
1071 PHE   ( 202-)  C
1382 PHE   (  77-)  D
1446 PHE   ( 141-)  D
1507 PHE   ( 202-)  D
1604 PHE   ( 299-)  D
1661 PHE   ( 356-)  D
1820 PHE   (  77-)  E
1884 PHE   ( 141-)  E
1945 PHE   ( 202-)  E
2253 PHE   (  77-)  F
2317 PHE   ( 141-)  F
2378 PHE   ( 202-)  F
2689 PHE   (  77-)  G
2753 PHE   ( 141-)  G
2814 PHE   ( 202-)  G
2968 PHE   ( 356-)  G
3126 PHE   (  77-)  H
3190 PHE   ( 141-)  H
3251 PHE   ( 202-)  H
3562 PHE   (  77-)  I
3626 PHE   ( 141-)  I
3687 PHE   ( 202-)  I
3841 PHE   ( 356-)  I
3999 PHE   (  77-)  J
4063 PHE   ( 141-)  J
4124 PHE   ( 202-)  J
4221 PHE   ( 299-)  J
4278 PHE   ( 356-)  J

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.

  69 ASP   (  76-)  A
 338 ASP   ( 345-)  A
 415 ASP   ( 422-)  A
 945 ASP   (  76-)  C
1381 ASP   (  76-)  D
1934 ASP   ( 191-)  E
2165 ASP   ( 422-)  E
2330 ASP   ( 154-)  F
2803 ASP   ( 191-)  G
3240 ASP   ( 191-)  H
4195 ASP   ( 273-)  J
4344 ASP   ( 422-)  J

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.

  91 GLU   (  98-)  A
 635 GLU   ( 204-)  B
 854 GLU   ( 423-)  B
 887 GLU   (  18-)  C
1091 GLU   ( 222-)  C
1354 GLU   (  49-)  D
1403 GLU   (  98-)  D
1728 GLU   ( 423-)  D
1841 GLU   (  98-)  E
2212 GLU   (  35-)  F
2350 GLU   ( 174-)  F
2398 GLU   ( 222-)  F
2418 GLU   ( 242-)  F
2710 GLU   (  98-)  G
3112 GLU   (  63-)  H
3271 GLU   ( 222-)  H
3583 GLU   (  98-)  I
3688 GLU   ( 203-)  I
3692 GLU   ( 207-)  I
3957 GLU   (  35-)  J
4164 GLU   ( 242-)  J
4358 GLU   ( 436-)  J

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 182 KCX   ( 189-)  A      CH     CX
 182 KCX   ( 189-)  A      OX1    OQ1
 182 KCX   ( 189-)  A      OX2    OQ2
 620 KCX   ( 189-)  B      CH     CX
 620 KCX   ( 189-)  B      OX1    OQ1
 620 KCX   ( 189-)  B      OX2    OQ2
1058 KCX   ( 189-)  C      CH     CX
1058 KCX   ( 189-)  C      OX1    OQ1
1058 KCX   ( 189-)  C      OX2    OQ2
1494 KCX   ( 189-)  D      CH     CX
1494 KCX   ( 189-)  D      OX1    OQ1
1494 KCX   ( 189-)  D      OX2    OQ2
1932 KCX   ( 189-)  E      CH     CX
1932 KCX   ( 189-)  E      OX1    OQ1
1932 KCX   ( 189-)  E      OX2    OQ2
2365 KCX   ( 189-)  F      CH     CX
2365 KCX   ( 189-)  F      OX1    OQ1
2365 KCX   ( 189-)  F      OX2    OQ2
2801 KCX   ( 189-)  G      CH     CX
2801 KCX   ( 189-)  G      OX1    OQ1
2801 KCX   ( 189-)  G      OX2    OQ2
3238 KCX   ( 189-)  H      CH     CX
3238 KCX   ( 189-)  H      OX1    OQ1
3238 KCX   ( 189-)  H      OX2    OQ2
3674 KCX   ( 189-)  I      CH     CX
3674 KCX   ( 189-)  I      OX1    OQ1
3674 KCX   ( 189-)  I      OX2    OQ2
4111 KCX   ( 189-)  J      CH     CX
4111 KCX   ( 189-)  J      OX1    OQ1
4111 KCX   ( 189-)  J      OX2    OQ2

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998978  0.000014  0.000034|
 |  0.000014  0.998941  0.000046|
 |  0.000034  0.000046  0.998793|
Proposed new scale matrix

 |  0.005777  0.000000  0.000000|
 |  0.000000  0.004063  0.000000|
 |  0.000000  0.000000  0.006924|
With corresponding cell

    A    = 173.103  B   = 246.105  C    = 144.418
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 173.287  B   = 246.377  C    = 144.589
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 174.696
(Under-)estimated Z-score: 9.741

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.

  69 ASP   (  76-)  A
  91 GLU   (  98-)  A
 115 ARG   ( 122-)  A
 338 ASP   ( 345-)  A
 415 ASP   ( 422-)  A
 497 ARG   (  66-)  B
 553 ARG   ( 122-)  B
 635 GLU   ( 204-)  B
 696 ARG   ( 265-)  B
 854 GLU   ( 423-)  B
 887 GLU   (  18-)  C
 935 ARG   (  66-)  C
 945 ASP   (  76-)  C
1091 GLU   ( 222-)  C
1354 GLU   (  49-)  D
1371 ARG   (  66-)  D
1381 ASP   (  76-)  D
1403 GLU   (  98-)  D
1427 ARG   ( 122-)  D
1570 ARG   ( 265-)  D
1728 GLU   ( 423-)  D
1738 ARG   ( 433-)  D
1841 GLU   (  98-)  E
1860 ARG   ( 117-)  E
1934 ASP   ( 191-)  E
And so on for a total of 56 lines.

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.

 923 THR   (  54-)  C    -3.1
2236 PRO   (  60-)  F    -3.0
3103 THR   (  54-)  H    -2.9
2837 THR   ( 225-)  G    -2.8
 656 THR   ( 225-)  B    -2.7
1968 THR   ( 225-)  E    -2.7
1094 THR   ( 225-)  C    -2.7
 218 THR   ( 225-)  A    -2.7
3274 THR   ( 225-)  H    -2.7
1530 THR   ( 225-)  D    -2.6
4030 ILE   ( 108-)  J    -2.6
4147 THR   ( 225-)  J    -2.5
 356 PHE   ( 363-)  A    -2.5
3848 PHE   ( 363-)  I    -2.5
3710 THR   ( 225-)  I    -2.5
2231 THR   (  54-)  F    -2.5
3980 LEU   (  58-)  J    -2.5
3539 THR   (  54-)  I    -2.5
 485 THR   (  54-)  B    -2.4
2975 PHE   ( 363-)  G    -2.4
1413 ILE   ( 108-)  D    -2.4
1359 THR   (  54-)  D    -2.4
2512 ILE   ( 336-)  F    -2.4
 794 PHE   ( 363-)  B    -2.4
 227 LEU   ( 234-)  A    -2.4
And so on for a total of 105 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.

  17 ASP   (  24-)  A  omega poor
  22 PHE   (  29-)  A  omega poor
  44 SER   (  51-)  A  Poor phi/psi
  45 THR   (  52-)  A  omega poor
  78 TRP   (  85-)  A  omega poor
  92 ALA   (  99-)  A  Poor phi/psi
 110 ARG   ( 117-)  A  omega poor
 152 GLY   ( 159-)  A  omega poor
 156 LYS   ( 163-)  A  PRO omega poor
 180 TYR   ( 187-)  A  omega poor
 188 THR   ( 195-)  A  Poor phi/psi
 225 ALA   ( 232-)  A  Poor phi/psi
 242 LEU   ( 249-)  A  omega poor
 277 MET   ( 284-)  A  Poor phi/psi
 302 GLY   ( 309-)  A  Poor phi/psi
 311 ALA   ( 318-)  A  Poor phi/psi
 350 TYR   ( 357-)  A  Poor phi/psi
 455 ASP   (  24-)  B  omega poor
 460 PHE   (  29-)  B  omega poor
 482 SER   (  51-)  B  Poor phi/psi
 516 TRP   (  85-)  B  omega poor
 548 ARG   ( 117-)  B  omega poor
 583 ILE   ( 152-)  B  omega poor
 594 LYS   ( 163-)  B  PRO omega poor
 626 THR   ( 195-)  B  Poor phi/psi
And so on for a total of 131 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

2786 GLU   ( 174-)  G    0.35
1487 SER   ( 182-)  D    0.38

Warning: Unusual backbone conformations

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

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

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

   8 LYS   (  15-)  A      0
  16 ARG   (  23-)  A      0
  28 GLU   (  35-)  A      0
  43 SER   (  50-)  A      0
  44 SER   (  51-)  A      0
  45 THR   (  52-)  A      0
  48 TRP   (  55-)  A      0
  52 TYR   (  59-)  A      0
  54 TRP   (  61-)  A      0
  55 TYR   (  62-)  A      0
  68 TYR   (  75-)  A      0
  69 ASP   (  76-)  A      0
  73 MET   (  80-)  A      0
  75 ASP   (  82-)  A      0
  77 SER   (  84-)  A      0
  86 PHE   (  93-)  A      0
  87 HIS   (  94-)  A      0
  91 GLU   (  98-)  A      0
  92 ALA   (  99-)  A      0
  93 ASN   ( 100-)  A      0
 101 ILE   ( 108-)  A      0
 102 ALA   ( 109-)  A      0
 104 ASN   ( 111-)  A      0
 108 MET   ( 115-)  A      0
 117 GLU   ( 124-)  A      0
And so on for a total of 1504 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!

2980 GLY   ( 368-)  G   2.79   11
2501 GLY   ( 325-)  F   2.45   22
1194 GLY   ( 325-)  C   2.29   24
3810 GLY   ( 325-)  I   2.22   25
 318 GLY   ( 325-)  A   2.19   25
4247 GLY   ( 325-)  J   2.19   28
 756 GLY   ( 325-)  B   2.12   35
1630 GLY   ( 325-)  D   2.04   32
2937 GLY   ( 325-)  G   1.97   36
3374 GLY   ( 325-)  H   1.96   35
2068 GLY   ( 325-)  E   1.88   34
2136 GLY   ( 393-)  E   1.56   80
4315 GLY   ( 393-)  J   1.55   80
 824 GLY   ( 393-)  B   1.54   80
1262 GLY   ( 393-)  C   1.53   80
 386 GLY   ( 393-)  A   1.50   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 370 PRO   ( 377-)  A    0.18 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].

 587 PRO   ( 156-)  B  -121.1 half-chair C-delta/C-gamma (-126 degrees)
1025 PRO   ( 156-)  C  -122.6 half-chair C-delta/C-gamma (-126 degrees)
1246 PRO   ( 377-)  C  -118.9 half-chair C-delta/C-gamma (-126 degrees)
2163 PRO   ( 420-)  E   105.2 envelop C-beta (108 degrees)
2236 PRO   (  60-)  F   128.0 half-chair C-beta/C-alpha (126 degrees)
2278 PRO   ( 102-)  F   103.7 envelop C-beta (108 degrees)
2574 PRO   ( 398-)  F   114.0 envelop C-beta (108 degrees)
2577 PRO   ( 401-)  F   101.9 envelop C-beta (108 degrees)
2596 PRO   ( 420-)  F    99.8 envelop C-beta (108 degrees)
2768 PRO   ( 156-)  G  -118.4 half-chair C-delta/C-gamma (-126 degrees)
3032 PRO   ( 420-)  G   105.4 envelop C-beta (108 degrees)
3341 PRO   ( 292-)  H    40.7 envelop C-delta (36 degrees)
3426 PRO   ( 377-)  H  -118.5 half-chair C-delta/C-gamma (-126 degrees)
4320 PRO   ( 398-)  J     0.7 envelop N (0 degrees)
4323 PRO   ( 401-)  J   104.1 envelop C-beta (108 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.

4319 HIS   ( 397-)  J      ND1 <-> 4320 PRO   ( 398-)  J      CD     0.84    2.26  INTRA BF
4095 PHE   ( 173-)  J      CE2 <-> 4131 MET   ( 209-)  J      CE     0.83    2.37  INTRA
2255 ASP   (  79-)  F      CA  <-> 2261 TRP   (  85-)  F      NE1    0.62    2.48  INTRA BF
1363 LEU   (  58-)  D      CA  <-> 4390 HOH   ( 738 )  D      O      0.55    2.25  INTRA BF
1018 MET   ( 149-)  C      CE  <-> 1120 HIS   ( 251-)  C      CE1    0.54    2.66  INTRA
3466 GLN   ( 417-)  H      CB  <-> 3468 ILE   ( 419-)  H      CD1    0.54    2.66  INTRA BF
1369 GLN   (  64-)  D      CD  <-> 4390 HOH   ( 631 )  D      O      0.53    2.27  INTRA
1369 GLN   (  64-)  D      CB  <-> 4390 HOH   ( 631 )  D      O      0.53    2.27  INTRA
2761 MET   ( 149-)  G      CE  <-> 2863 HIS   ( 251-)  G      CE1    0.48    2.72  INTRA
1032 LYS   ( 163-)  C      N   <-> 1264 LEU   ( 395-)  C      CD2    0.48    2.62  INTRA
2114 HIS   ( 371-)  E      ND1 <-> 2116 GLY   ( 373-)  E      N      0.48    2.52  INTRA
3212 LYS   ( 163-)  H      N   <-> 3444 LEU   ( 395-)  H      CD2    0.47    2.63  INTRA
2254 HIS   (  78-)  F      C   <-> 2261 TRP   (  85-)  F      CD1    0.47    2.73  INTRA BF
2255 ASP   (  79-)  F      CB  <-> 2261 TRP   (  85-)  F      NE1    0.47    2.63  INTRA BF
3300 HIS   ( 251-)  H      NE2 <-> 3361 GLN   ( 312-)  H      NE2    0.46    2.54  INTRA BL
1314 TYR   (   9-)  D      CD2 <-> 1422 ARG   ( 117-)  D      NH2    0.46    2.64  INTRA
2140 HIS   ( 397-)  E      ND1 <-> 2141 PRO   ( 398-)  E      CD     0.44    2.66  INTRA BF
3168 LYS   ( 119-)  H      CB  <-> 4394 HOH   ( 669 )  H      O      0.44    2.36  INTRA
4000 HIS   (  78-)  J      ND1 <-> 4396 HOH   ( 687 )  J      O      0.44    2.26  INTRA
2255 ASP   (  79-)  F      CA  <-> 2261 TRP   (  85-)  F      CD1    0.41    2.79  INTRA BF
2520 PRO   ( 344-)  F      C   <-> 4392 HOH   ( 560 )  F      O      0.41    2.39  INTRA
2552 GLN   ( 376-)  F      CG  <-> 4392 HOH   ( 639 )  F      O      0.41    2.39  INTRA
3802 THR   ( 317-)  I      N   <-> 4395 HOH   ( 621 )  I      O      0.41    2.29  INTRA
3980 LEU   (  58-)  J      CD2 <-> 3981 TYR   (  59-)  J      N      0.40    2.60  INTRA
2301 ASP   ( 125-)  F      OD1 <-> 2302 LEU   ( 126-)  F      N      0.40    2.20  INTRA
And so on for a total of 823 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

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.

 490 TYR   (  59-)  B      -7.22
2066 LEU   ( 323-)  E      -7.09
1364 TYR   (  59-)  D      -7.08
 754 LEU   ( 323-)  B      -6.98
4245 LEU   ( 323-)  J      -6.96
2935 LEU   ( 323-)  G      -6.90
 316 LEU   ( 323-)  A      -6.83
1192 LEU   ( 323-)  C      -6.83
1628 LEU   ( 323-)  D      -6.77
3808 LEU   ( 323-)  I      -6.76
3372 LEU   ( 323-)  H      -6.75
2499 LEU   ( 323-)  F      -6.73
2671 TYR   (  59-)  G      -6.72
 283 ARG   ( 290-)  A      -6.71
 928 TYR   (  59-)  C      -6.71
3339 ARG   ( 290-)  H      -6.63
 721 ARG   ( 290-)  B      -6.62
3108 TYR   (  59-)  H      -6.62
1159 ARG   ( 290-)  C      -6.58
1802 TYR   (  59-)  E      -6.53
2033 ARG   ( 290-)  E      -6.47
2902 ARG   ( 290-)  G      -6.43
1595 ARG   ( 290-)  D      -6.38
4212 ARG   ( 290-)  J      -6.25
3775 ARG   ( 290-)  I      -6.23
And so on for a total of 109 lines.

Warning: Abnormal packing environment for sequential residues

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

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

 315 LYS   ( 322-)  A       317 - GLU    324- ( A)         -5.89
 753 LYS   ( 322-)  B       755 - GLU    324- ( B)         -6.05
1191 LYS   ( 322-)  C      1193 - GLU    324- ( C)         -5.96
1627 LYS   ( 322-)  D      1629 - GLU    324- ( D)         -5.97
1741 GLU   ( 436-)  D      1743 - TRP    438- ( D)         -4.39
1800 THR   (  57-)  E      1802 - TYR     59- ( E)         -5.53
2065 LYS   ( 322-)  E      2067 - GLU    324- ( E)         -6.08
2498 LYS   ( 322-)  F      2500 - GLU    324- ( F)         -5.99
2934 LYS   ( 322-)  G      2936 - GLU    324- ( G)         -5.96
3106 THR   (  57-)  H      3108 - TYR     59- ( H)         -5.50
3371 LYS   ( 322-)  H      3373 - GLU    324- ( H)         -5.82
3807 LYS   ( 322-)  I      3809 - GLU    324- ( I)         -5.88
3979 THR   (  57-)  J      3981 - TYR     59- ( J)         -5.35
4244 LYS   ( 322-)  J      4246 - GLU    324- ( J)         -6.01
4358 GLU   ( 436-)  J      4360 - TRP    438- ( J)         -4.60

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

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.

  52 TYR   (  59-)  A   -3.46
3544 TYR   (  59-)  I   -3.24
2670 LEU   (  58-)  G   -3.02
2198 LYS   (  21-)  F   -3.02
2462 ALA   ( 286-)  F   -2.96
 489 LEU   (  58-)  B   -2.96
 717 ALA   ( 286-)  B   -2.88
3335 ALA   ( 286-)  H   -2.87
2235 TYR   (  59-)  F   -2.85
  51 LEU   (  58-)  A   -2.75
2194 TYR   (  17-)  F   -2.63
3444 LEU   ( 395-)  H   -2.52
2711 ALA   (  99-)  G   -2.50

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

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.

4387 HOH   ( 659 )  A      O     86.28  -47.44   23.33
4388 HOH   ( 713 )  B      O     75.55    6.03  -35.00
4390 HOH   ( 657 )  D      O     99.64   40.35   70.68
4390 HOH   ( 711 )  D      O     86.40   29.05   37.01
4390 HOH   ( 720 )  D      O     92.30   13.38   55.84
4391 HOH   ( 683 )  E      O     63.73  -43.38   60.36
4391 HOH   ( 692 )  E      O     91.46  -12.25   66.69
4391 HOH   ( 716 )  E      O     84.04  -15.30   40.87
4392 HOH   ( 576 )  F      O      1.24   47.21   67.13
4394 HOH   ( 694 )  H      O     -6.75  -31.10   62.72
4395 HOH   ( 673 )  I      O     -1.71  -13.10   85.91
4395 HOH   ( 750 )  I      O     -1.83  -27.39   99.39
4395 HOH   ( 751 )  I      O      0.20  -27.67   97.52

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.

4387 HOH   ( 580 )  A      O
4390 HOH   ( 621 )  D      O
4390 HOH   ( 631 )  D      O
4392 HOH   ( 587 )  F      O
4396 HOH   ( 747 )  J      O
ERROR. No convergence in HB2STD
Old,New value: 4575.365 4575.390

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.

 340 ASN   ( 347-)  A
 347 GLN   ( 354-)  A
 670 GLN   ( 239-)  B
 745 HIS   ( 314-)  B
 785 GLN   ( 354-)  B
 848 GLN   ( 417-)  B
1223 GLN   ( 354-)  C
1599 HIS   ( 294-)  D
1617 GLN   ( 312-)  D
1619 HIS   ( 314-)  D
1659 GLN   ( 354-)  D
1694 GLN   ( 389-)  D
1745 HIS   ( 440-)  D
2057 HIS   ( 314-)  E
2094 HIS   ( 351-)  E
2097 GLN   ( 354-)  E
2132 GLN   ( 389-)  E
2470 HIS   ( 294-)  F
2508 GLN   ( 332-)  F
2530 GLN   ( 354-)  F
2565 GLN   ( 389-)  F
2891 HIS   ( 279-)  G
2966 GLN   ( 354-)  G
3363 HIS   ( 314-)  H
3403 GLN   ( 354-)  H
3817 GLN   ( 332-)  I
3839 GLN   ( 354-)  I
3874 GLN   ( 389-)  I
3986 GLN   (  64-)  J
4115 ASN   ( 193-)  J
4236 HIS   ( 314-)  J
4276 GLN   ( 354-)  J

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.

  47 THR   (  54-)  A      OG1
 104 ASN   ( 111-)  A      ND2
 114 LEU   ( 121-)  A      N
 156 LYS   ( 163-)  A      N
 156 LYS   ( 163-)  A      NZ
 158 LYS   ( 165-)  A      NZ
 159 VAL   ( 166-)  A      N
 182 KCX   ( 189-)  A      OX1
 192 TYR   ( 199-)  A      N
 193 ASN   ( 200-)  A      ND2
 244 HIS   ( 251-)  A      NE2
 275 ARG   ( 282-)  A      NE
 311 ALA   ( 318-)  A      N
 315 LYS   ( 322-)  A      NZ
 360 SER   ( 367-)  A      OG
 362 GLY   ( 369-)  A      N
 371 VAL   ( 378-)  A      N
 382 GLN   ( 389-)  A      NE2
 384 GLY   ( 391-)  A      N
 385 GLY   ( 392-)  A      N
 440 TYR   (   9-)  B      N
 514 GLY   (  83-)  B      N
 519 ARG   (  88-)  B      NH1
 542 ASN   ( 111-)  B      ND2
 552 LEU   ( 121-)  B      N
And so on for a total of 206 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.

 248 ASP   ( 255-)  A      OD1
 248 ASP   ( 255-)  A      OD2
 307 HIS   ( 314-)  A      ND1
 686 ASP   ( 255-)  B      OD1
 686 ASP   ( 255-)  B      OD2
 710 HIS   ( 279-)  B      ND1
 743 GLN   ( 312-)  B      OE1
1124 ASP   ( 255-)  C      OD1
1124 ASP   ( 255-)  C      OD2
1183 HIS   ( 314-)  C      ND1
1354 GLU   (  49-)  D      OE1
1560 ASP   ( 255-)  D      OD1
1560 ASP   ( 255-)  D      OD2
1998 ASP   ( 255-)  E      OD1
2022 HIS   ( 279-)  E      NE2
2431 ASP   ( 255-)  F      OD1
2431 ASP   ( 255-)  F      OD2
2490 HIS   ( 314-)  F      ND1
2867 ASP   ( 255-)  G      OD1
2867 ASP   ( 255-)  G      OD2
2926 HIS   ( 314-)  G      ND1
3304 ASP   ( 255-)  H      OD1
3328 HIS   ( 279-)  H      ND1
3361 GLN   ( 312-)  H      OE1
3740 ASP   ( 255-)  I      OD1
3740 ASP   ( 255-)  I      OD2
3799 HIS   ( 314-)  I      ND1
4177 ASP   ( 255-)  J      OD1
4201 HIS   ( 279-)  J      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+.

4379  MG   ( 445-)  G     0.68   1.17 Is perhaps CA *2
4381  MG   ( 445-)  H     0.63   1.08 Is perhaps CA *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.

4387 HOH   ( 567 )  A      O  0.89  K  4 NCS 1/1
4387 HOH   ( 620 )  A      O  1.04  K  4 ION-B
4387 HOH   ( 667 )  A      O  0.87  K  4 NCS 1/1
4388 HOH   ( 567 )  B      O  0.89  K  4 NCS 1/1
4389 HOH   ( 688 )  C      O  0.95  K  4 NCS 3/3
4390 HOH   ( 722 )  D      O  0.85  K  4 Ion-B
4390 HOH   ( 734 )  D      O  0.98  K  4 NCS 2/2
4390 HOH   ( 736 )  D      O  1.08  K  5 NCS 3/3
4391 HOH   ( 636 )  E      O  1.08  K  4 Ion-B NCS 5/5
4391 HOH   ( 708 )  E      O  1.07  K  4 NCS 4/4
4392 HOH   ( 600 )  F      O  0.96  K  4 Ion-B
4393 HOH   ( 516 )  G      O  0.92  K  4 NCS 5/5
4393 HOH   ( 613 )  G      O  0.99  K  4 Ion-B NCS 8/8
4395 HOH   ( 663 )  I      O  1.05  K  4 H2O-B NCS 1/1
4396 HOH   ( 584 )  J      O  1.09  K  4 H2O-B NCS 4/4
4396 HOH   ( 685 )  J      O  0.93  K  4 NCS 9/9
4396 HOH   ( 705 )  J      O  0.94  K  4 Ion-B NCS 8/8
4396 HOH   ( 746 )  J      O  0.86  K  5 Ion-B NCS 8/8

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.

 226 ASP   ( 233-)  A   H-bonding suggests Asn
 248 ASP   ( 255-)  A   H-bonding suggests Asn; but Alt-Rotamer
 686 ASP   ( 255-)  B   H-bonding suggests Asn; but Alt-Rotamer
 844 ASP   ( 413-)  B   H-bonding suggests Asn
1023 ASP   ( 154-)  C   H-bonding suggests Asn; but Alt-Rotamer
1124 ASP   ( 255-)  C   H-bonding suggests Asn; but Alt-Rotamer
1282 ASP   ( 413-)  C   H-bonding suggests Asn
1512 GLU   ( 207-)  D   H-bonding suggests Gln
1551 ASP   ( 246-)  D   H-bonding suggests Asn
1560 ASP   ( 255-)  D   H-bonding suggests Asn; but Alt-Rotamer
1753 ASP   (  10-)  E   H-bonding suggests Asn
1957 ASP   ( 214-)  E   H-bonding suggests Asn
1998 ASP   ( 255-)  E   H-bonding suggests Asn; but Alt-Rotamer
2016 ASP   ( 273-)  E   H-bonding suggests Asn
2156 ASP   ( 413-)  E   H-bonding suggests Asn
2431 ASP   ( 255-)  F   H-bonding suggests Asn; but Alt-Rotamer
2766 ASP   ( 154-)  G   H-bonding suggests Asn; but Alt-Rotamer
2867 ASP   ( 255-)  G   H-bonding suggests Asn; but Alt-Rotamer
3025 ASP   ( 413-)  G   H-bonding suggests Asn; but Alt-Rotamer
3203 ASP   ( 154-)  H   H-bonding suggests Asn; but Alt-Rotamer
3304 ASP   ( 255-)  H   H-bonding suggests Asn; but Alt-Rotamer
3462 ASP   ( 413-)  H   H-bonding suggests Asn
3503 GLU   (  18-)  I   H-bonding suggests Gln
3731 ASP   ( 246-)  I   H-bonding suggests Asn
3740 ASP   ( 255-)  I   H-bonding suggests Asn; but Alt-Rotamer
4177 ASP   ( 255-)  J   H-bonding suggests Asn; but Alt-Rotamer
4335 ASP   ( 413-)  J   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 :  -0.596
  2nd generation packing quality :  -0.927
  Ramachandran plot appearance   :  -1.154
  chi-1/chi-2 rotamer normality  :  -1.100
  Backbone conformation          :  -0.070

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.313 (tight)
  Bond angles                    :   0.545 (tight)
  Omega angle restraints         :   0.951
  Side chain planarity           :   0.287 (tight)
  Improper dihedral distribution :   0.524
  B-factor distribution          :   0.354
  Inside/Outside distribution    :   1.025

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :   0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.313 (tight)
  Bond angles                    :   0.545 (tight)
  Omega angle restraints         :   0.951
  Side chain planarity           :   0.287 (tight)
  Improper dihedral distribution :   0.524
  B-factor distribution          :   0.354
  Inside/Outside distribution    :   1.025
==============

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.