WHAT IF Check report

This file was created 2012-09-07 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 pdb4fzh.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 : 0.603
CA-only RMS fit for the two chains : 0.374

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 : 0.570
CA-only RMS fit for the two chains : 0.385

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 : 0.698
CA-only RMS fit for the two chains : 0.465

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 : 0.675
CA-only RMS fit for the two chains : 0.448

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 : 0.582
CA-only RMS fit for the two chains : 0.413

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

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1947 NAG   ( 703-)  A  -   O4  bound to 1948 NAG   ( 704-)  A  -   C1
1951 NAG   ( 703-)  B  -   O4  bound to 1952 NAG   ( 704-)  B  -   C1
1954 NAG   ( 702-)  C  -   O4  bound to 1955 NAG   ( 703-)  C  -   C1
1958 NAG   ( 703-)  D  -   O4  bound to 1959 NAG   ( 704-)  D  -   C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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'.

 449 ARG   ( 578-)  A      CG
 449 ARG   ( 578-)  A      CD
 449 ARG   ( 578-)  A      NE
 449 ARG   ( 578-)  A      CZ
 449 ARG   ( 578-)  A      NH1
 449 ARG   ( 578-)  A      NH2
 450 LEU   ( 579-)  A      CG
 450 LEU   ( 579-)  A      CD1
 450 LEU   ( 579-)  A      CD2
 451 SER   ( 580-)  A      OG
 452 GLN   ( 581-)  A      CG
 452 GLN   ( 581-)  A      CD
 452 GLN   ( 581-)  A      OE1
 452 GLN   ( 581-)  A      NE2
 453 LEU   ( 582-)  A      CG
 453 LEU   ( 582-)  A      CD1
 453 LEU   ( 582-)  A      CD2
 454 ARG   ( 583-)  A      CG
 454 ARG   ( 583-)  A      CD
 454 ARG   ( 583-)  A      NE
 454 ARG   ( 583-)  A      CZ
 454 ARG   ( 583-)  A      NH1
 454 ARG   ( 583-)  A      NH2
 935 ARG   ( 578-)  B      CG
 935 ARG   ( 578-)  B      CD
And so on for a total of 92 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

   1 GLY   ( 124-)  A    High
   2 ALA   ( 125-)  A    High
   3 PRO   ( 126-)  A    High
   4 ILE   ( 127-)  A    High
   5 HIS   ( 128-)  A    High
   6 ASP   ( 129-)  A    High
   7 PRO   ( 130-)  A    High
   8 ASP   ( 131-)  A    High
   9 TYR   ( 132-)  A    High
  10 ILE   ( 133-)  A    High
  11 GLY   ( 134-)  A    High
  12 GLY   ( 135-)  A    High
  13 ILE   ( 136-)  A    High
  14 GLY   ( 137-)  A    High
  15 LYS   ( 138-)  A    High
  16 GLU   ( 139-)  A    High
  17 LEU   ( 140-)  A    High
  18 ILE   ( 141-)  A    High
  19 VAL   ( 142-)  A    High
  20 ASP   ( 143-)  A    High
  21 ASP   ( 144-)  A    High
  22 ALA   ( 145-)  A    High
  23 SER   ( 146-)  A    High
  24 ASP   ( 147-)  A    High
  25 VAL   ( 148-)  A    High
And so on for a total of 1919 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: 25

Crystal temperature (K) : 77.200

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: Tyrosine convention problem

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

  82 TYR   ( 205-)  A
 158 TYR   ( 281-)  A
 176 TYR   ( 299-)  A
 211 TYR   ( 334-)  A
 304 TYR   ( 427-)  A
 403 TYR   ( 526-)  A
 418 TYR   ( 541-)  A
 550 TYR   ( 187-)  B
 644 TYR   ( 281-)  B
 713 TYR   ( 350-)  B
 790 TYR   ( 427-)  B
 833 TYR   ( 470-)  B
 889 TYR   ( 526-)  B
1001 TYR   ( 152-)  C
1054 TYR   ( 205-)  C
1166 TYR   ( 317-)  C
1375 TYR   ( 526-)  C
1390 TYR   ( 541-)  C
1685 TYR   ( 350-)  D
1755 TYR   ( 420-)  D
1762 TYR   ( 427-)  D
1809 TYR   ( 474-)  D
1861 TYR   ( 526-)  D
1876 TYR   ( 541-)  D

Warning: Phenylalanine convention problem

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

  28 PHE   ( 151-)  A
  97 PHE   ( 220-)  A
 289 PHE   ( 412-)  A
 355 PHE   ( 478-)  A
 430 PHE   ( 553-)  A
 466 PHE   ( 595-)  A
 514 PHE   ( 151-)  B
 541 PHE   ( 178-)  B
 670 PHE   ( 307-)  B
 851 PHE   ( 488-)  B
 916 PHE   ( 553-)  B
1000 PHE   ( 151-)  C
1069 PHE   ( 220-)  C
1126 PHE   ( 277-)  C
1163 PHE   ( 314-)  C
1261 PHE   ( 412-)  C
1337 PHE   ( 488-)  C
1355 PHE   ( 506-)  C
1486 PHE   ( 151-)  D
1491 PHE   ( 156-)  D
1513 PHE   ( 178-)  D
1699 PHE   ( 364-)  D
1823 PHE   ( 488-)  D
1867 PHE   ( 532-)  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.

  24 ASP   ( 147-)  A
  75 ASP   ( 198-)  A
 138 ASP   ( 261-)  A
 459 ASP   ( 588-)  A
 460 ASP   ( 589-)  A
 561 ASP   ( 198-)  B
 594 ASP   ( 231-)  B
 624 ASP   ( 261-)  B
 641 ASP   ( 278-)  B
 808 ASP   ( 445-)  B
 946 ASP   ( 589-)  B
1047 ASP   ( 198-)  C
1080 ASP   ( 231-)  C
1110 ASP   ( 261-)  C
1176 ASP   ( 327-)  C
1294 ASP   ( 445-)  C
1343 ASP   ( 494-)  C
1431 ASP   ( 588-)  C
1432 ASP   ( 589-)  C
1482 ASP   ( 147-)  D
1533 ASP   ( 198-)  D
1596 ASP   ( 261-)  D
1613 ASP   ( 278-)  D
1662 ASP   ( 327-)  D
1780 ASP   ( 445-)  D
1829 ASP   ( 494-)  D
1918 ASP   ( 589-)  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.

 135 GLU   ( 258-)  A
 136 GLU   ( 259-)  A
 208 GLU   ( 331-)  A
 278 GLU   ( 401-)  A
 432 GLU   ( 555-)  A
 478 GLU   ( 607-)  A
 619 GLU   ( 256-)  B
 621 GLU   ( 258-)  B
 622 GLU   ( 259-)  B
 694 GLU   ( 331-)  B
 764 GLU   ( 401-)  B
1105 GLU   ( 256-)  C
1107 GLU   ( 258-)  C
1108 GLU   ( 259-)  C
1180 GLU   ( 331-)  C
1250 GLU   ( 401-)  C
1396 GLU   ( 547-)  C
1450 GLU   ( 607-)  C
1591 GLU   ( 256-)  D
1594 GLU   ( 259-)  D
1666 GLU   ( 331-)  D
1736 GLU   ( 401-)  D

Geometric checks

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.

 431 GLY   ( 554-)  A      N    CA   C   124.69    4.2
 465 ILE   ( 594-)  A      N    CA   C   125.42    5.1
 917 GLY   ( 554-)  B      N    CA   C   125.06    4.3

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  24 ASP   ( 147-)  A
  75 ASP   ( 198-)  A
 135 GLU   ( 258-)  A
 136 GLU   ( 259-)  A
 138 ASP   ( 261-)  A
 208 GLU   ( 331-)  A
 278 GLU   ( 401-)  A
 432 GLU   ( 555-)  A
 459 ASP   ( 588-)  A
 460 ASP   ( 589-)  A
 478 GLU   ( 607-)  A
 561 ASP   ( 198-)  B
 594 ASP   ( 231-)  B
 619 GLU   ( 256-)  B
 621 GLU   ( 258-)  B
 622 GLU   ( 259-)  B
 624 ASP   ( 261-)  B
 641 ASP   ( 278-)  B
 694 GLU   ( 331-)  B
 764 GLU   ( 401-)  B
 808 ASP   ( 445-)  B
 946 ASP   ( 589-)  B
1047 ASP   ( 198-)  C
1080 ASP   ( 231-)  C
1105 GLU   ( 256-)  C
1107 GLU   ( 258-)  C
1108 GLU   ( 259-)  C
1110 ASP   ( 261-)  C
1176 ASP   ( 327-)  C
1180 GLU   ( 331-)  C
1250 GLU   ( 401-)  C
1294 ASP   ( 445-)  C
1343 ASP   ( 494-)  C
1396 GLU   ( 547-)  C
1431 ASP   ( 588-)  C
1432 ASP   ( 589-)  C
1450 GLU   ( 607-)  C
1482 ASP   ( 147-)  D
1533 ASP   ( 198-)  D
1591 GLU   ( 256-)  D
1594 GLU   ( 259-)  D
1596 ASP   ( 261-)  D
1613 ASP   ( 278-)  D
1662 ASP   ( 327-)  D
1666 GLU   ( 331-)  D
1736 GLU   ( 401-)  D
1780 ASP   ( 445-)  D
1829 ASP   ( 494-)  D
1918 ASP   ( 589-)  D

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.

 467 CYS   ( 596-)  A      C     -6.2    -8.94     0.22
1439 CYS   ( 596-)  C      C     -6.9    -9.94     0.22
The average deviation= 0.698

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.

1932 GLU   ( 603-)  D    5.73
 465 ILE   ( 594-)  A    5.33
1437 ILE   ( 594-)  C    4.26
 917 GLY   ( 554-)  B    4.12

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.

1886 THR   ( 551-)  D    -3.6
 830 THR   ( 467-)  B    -3.5
 914 THR   ( 551-)  B    -3.5
 428 THR   ( 551-)  A    -3.5
 344 THR   ( 467-)  A    -3.4
1931 THR   ( 602-)  D    -3.3
1802 THR   ( 467-)  D    -3.3
 473 THR   ( 602-)  A    -3.2
 703 TYR   ( 340-)  B    -3.1
 437 PRO   ( 560-)  A    -2.8
1562 ILE   ( 227-)  D    -2.6
1895 PRO   ( 560-)  D    -2.6
   4 ILE   ( 127-)  A    -2.6
 114 SER   ( 237-)  A    -2.6
  60 THR   ( 183-)  A    -2.6
  52 ILE   ( 175-)  A    -2.6
 883 SER   ( 520-)  B    -2.5
 800 THR   ( 437-)  B    -2.5
1675 TYR   ( 340-)  D    -2.5
 832 VAL   ( 469-)  B    -2.4
1334 ARG   ( 485-)  C    -2.4
1296 PHE   ( 447-)  C    -2.4
1676 ASN   ( 341-)  D    -2.4
1318 VAL   ( 469-)  C    -2.4
1348 LEU   ( 499-)  C    -2.4
And so on for a total of 101 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 ILE   ( 127-)  A  Poor phi/psi
  47 SER   ( 170-)  A  Poor phi/psi
  50 THR   ( 173-)  A  omega poor
  51 ARG   ( 174-)  A  omega poor
  52 ILE   ( 175-)  A  Poor phi/psi
  86 GLY   ( 209-)  A  omega poor
 160 GLU   ( 283-)  A  omega poor
 163 LEU   ( 286-)  A  omega poor
 164 ASP   ( 287-)  A  omega poor
 169 PHE   ( 292-)  A  omega poor
 179 VAL   ( 302-)  A  Poor phi/psi
 180 GLY   ( 303-)  A  Poor phi/psi, omega poor
 187 ASN   ( 310-)  A  Poor phi/psi
 200 ASN   ( 323-)  A  Poor phi/psi
 211 TYR   ( 334-)  A  Poor phi/psi
 218 ASN   ( 341-)  A  Poor phi/psi
 246 VAL   ( 369-)  A  omega poor
 262 ASP   ( 385-)  A  Poor phi/psi
 296 SER   ( 419-)  A  Poor phi/psi
 302 LEU   ( 425-)  A  omega poor
 310 ASN   ( 433-)  A  Poor phi/psi
 311 LYS   ( 434-)  A  Poor phi/psi
 321 PHE   ( 444-)  A  omega poor
 344 THR   ( 467-)  A  Poor phi/psi
 359 HIS   ( 482-)  A  Poor phi/psi
And so on for a total of 144 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.095

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.

 689 SER   ( 326-)  B    0.36
1133 LYS   ( 284-)  C    0.36

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!

   3 PRO   ( 126-)  A      0
   4 ILE   ( 127-)  A      0
   5 HIS   ( 128-)  A      0
  10 ILE   ( 133-)  A      0
  13 ILE   ( 136-)  A      0
  17 LEU   ( 140-)  A      0
  20 ASP   ( 143-)  A      0
  21 ASP   ( 144-)  A      0
  28 PHE   ( 151-)  A      0
  32 ALA   ( 155-)  A      0
  33 PHE   ( 156-)  A      0
  36 HIS   ( 159-)  A      0
  39 PHE   ( 162-)  A      0
  43 PRO   ( 166-)  A      0
  44 THR   ( 167-)  A      0
  47 SER   ( 170-)  A      0
  51 ARG   ( 174-)  A      0
  52 ILE   ( 175-)  A      0
  60 THR   ( 183-)  A      0
  61 HIS   ( 184-)  A      0
  66 HIS   ( 189-)  A      0
  70 LEU   ( 193-)  A      0
  71 SER   ( 194-)  A      0
  73 CYS   ( 196-)  A      0
  76 HIS   ( 199-)  A      0
And so on for a total of 963 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!

1248 GLY   ( 399-)  C   2.53   22
 276 GLY   ( 399-)  A   2.51   11
 121 PRO   ( 244-)  A   1.77   12
1153 GLY   ( 304-)  C   1.65   13
1465 PRO   ( 130-)  D   1.64   14
1640 GLY   ( 305-)  D   1.62   38

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].

 144 PRO   ( 267-)  A   103.4 envelop C-beta (108 degrees)
 202 PRO   ( 325-)  A    99.0 envelop C-beta (108 degrees)
 529 PRO   ( 166-)  B   106.5 envelop C-beta (108 degrees)
 791 PRO   ( 428-)  B  -122.1 half-chair C-delta/C-gamma (-126 degrees)
1465 PRO   ( 130-)  D    99.1 envelop C-beta (108 degrees)
1763 PRO   ( 428-)  D  -117.8 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

1803 GLY   ( 468-)  D      O    <->  1833 ARG   ( 498-)  D      NH2  0.68    2.02  INTRA BF
 882 SER   ( 519-)  B      N    <->   944 LYS   ( 587-)  B      O    0.68    2.02  INTRA BL
1574 SER   ( 239-)  D      OG   <->  1638 GLY   ( 303-)  D      O    0.65    1.75  INTRA BF
 694 GLU   ( 331-)  B      OE1  <->   731 ARG   ( 368-)  B      NH2  0.64    2.06  INTRA BF
  51 ARG   ( 174-)  A      NH2  <->   486 TRP   ( 615-)  A      CZ2  0.56    2.54  INTRA BL
1568 GLN   ( 233-)  D      OE1  <->  1588 LYS   ( 253-)  D      NZ   0.55    2.15  INTRA BF
1343 ASP   ( 494-)  C      OD2  <->  1448 ARG   ( 605-)  C      NH2  0.55    2.15  INTRA BF
1180 GLU   ( 331-)  C      OE1  <->  1217 ARG   ( 368-)  C      NH2  0.55    2.15  INTRA BF
1854 SER   ( 519-)  D      N    <->  1916 LYS   ( 587-)  D      O    0.53    2.17  INTRA BF
 779 ARG   ( 416-)  B      NH2  <->   831 GLY   ( 468-)  B      O    0.51    2.19  INTRA BL
1787 SER   ( 452-)  D      OG   <->  1802 THR   ( 467-)  D      OG1  0.51    1.89  INTRA BF
1736 GLU   ( 401-)  D      OE2  <->  1751 ARG   ( 416-)  D      NH1  0.50    2.20  INTRA BF
1677 ASP   ( 342-)  D      OD2  <->  1795 ARG   ( 460-)  D      NH1  0.48    2.22  INTRA BF
  65 THR   ( 188-)  A      OG1  <->    81 GLN   ( 204-)  A      NE2  0.46    2.24  INTRA BL
 537 ARG   ( 174-)  B      NH2  <->   972 TRP   ( 615-)  B      CZ2  0.45    2.65  INTRA BL
1677 ASP   ( 342-)  D      CG   <->  1795 ARG   ( 460-)  D      NH1  0.45    2.65  INTRA BF
1037 THR   ( 188-)  C      OG1  <->  1053 GLN   ( 204-)  C      NE2  0.44    2.26  INTRA BL
1514 ASP   ( 179-)  D      OD2  <->  1577 ALA   ( 242-)  D      N    0.44    2.26  INTRA BF
 460 ASP   ( 589-)  A      OD1  <->   462 VAL   ( 591-)  A      N    0.44    2.26  INTRA BL
1833 ARG   ( 498-)  D      CZ   <->  1943 SER   ( 614-)  D      CB   0.43    2.77  INTRA BF
 138 ASP   ( 261-)  A      OD1  <->   141 SER   ( 264-)  A      OG   0.43    1.97  INTRA BL
 375 ARG   ( 498-)  A      NH1  <->   485 SER   ( 614-)  A      CA   0.40    2.70  INTRA BL
1368 SER   ( 519-)  C      N    <->  1430 LYS   ( 587-)  C      O    0.40    2.30  INTRA BF
 546 THR   ( 183-)  B      OG1  <->   547 HIS   ( 184-)  B      ND1  0.39    2.31  INTRA BL
1675 TYR   ( 340-)  D      CG   <->  1676 ASN   ( 341-)  D      N    0.39    2.61  INTRA BF
And so on for a total of 638 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.

1189 TYR   ( 340-)  C      -6.84
 217 TYR   ( 340-)  A      -6.68
1848 ARG   ( 513-)  D      -6.28
1674 ARG   ( 339-)  D      -6.26
1362 ARG   ( 513-)  C      -6.24
 390 ARG   ( 513-)  A      -6.21
 702 ARG   ( 339-)  B      -6.18
 876 ARG   ( 513-)  B      -5.95
1288 HIS   ( 439-)  C      -5.92
 154 PHE   ( 277-)  A      -5.90
1784 ARG   ( 449-)  D      -5.86
 640 PHE   ( 277-)  B      -5.82
1126 PHE   ( 277-)  C      -5.81
1309 ARG   ( 460-)  C      -5.77
 373 GLN   ( 496-)  A      -5.73
 240 ARG   ( 363-)  A      -5.72
1212 ARG   ( 363-)  C      -5.72
1345 GLN   ( 496-)  C      -5.65
1698 ARG   ( 363-)  D      -5.65
1815 ARG   ( 480-)  D      -5.62
 726 ARG   ( 363-)  B      -5.59
 859 GLN   ( 496-)  B      -5.55
1612 PHE   ( 277-)  D      -5.51
 326 ARG   ( 449-)  A      -5.42
1795 ARG   ( 460-)  D      -5.41
 823 ARG   ( 460-)  B      -5.41
 951 ILE   ( 594-)  B      -5.15
 703 TYR   ( 340-)  B      -5.11
 316 HIS   ( 439-)  A      -5.10
1675 TYR   ( 340-)  D      -5.05
1658 ASN   ( 323-)  D      -5.05
 812 ARG   ( 449-)  B      -5.04
 140 ASN   ( 263-)  A      -5.00
1923 ILE   ( 594-)  D      -5.00

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.

 970 ALA   ( 613-)  B       972 - TRP    615- ( B)         -4.37
1456 ALA   ( 613-)  C      1458 - TRP    615- ( C)         -4.41
1674 ARG   ( 339-)  D      1676 - ASN    341- ( D)         -5.17
1903 ASP   ( 568-)  D      1905 - GLY    570- ( D)         -4.22

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.

 936 LEU   ( 579-)  B   -2.96
1424 GLN   ( 581-)  C   -2.93
 938 GLN   ( 581-)  B   -2.91
1910 GLN   ( 581-)  D   -2.91
 452 GLN   ( 581-)  A   -2.85
1907 ARG   ( 578-)  D   -2.74
1421 ARG   ( 578-)  C   -2.73
1078 LEU   ( 229-)  C   -2.68
 449 ARG   ( 578-)  A   -2.68
1908 LEU   ( 579-)  D   -2.67
 997 VAL   ( 148-)  C   -2.56

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.

 451 SER   ( 580-)  A     -  454 ARG   ( 583-)  A        -2.23
 937 SER   ( 580-)  B     -  940 ARG   ( 583-)  B        -2.00
1423 SER   ( 580-)  C     - 1426 ARG   ( 583-)  C        -2.15
1909 SER   ( 580-)  D     - 1912 ARG   ( 583-)  D        -2.12

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: 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.

 149 HIS   ( 272-)  A
 157 GLN   ( 280-)  A
 340 ASN   ( 463-)  A
 359 HIS   ( 482-)  A
 377 ASN   ( 500-)  A
 597 ASN   ( 234-)  B
 845 HIS   ( 482-)  B
 977 HIS   ( 128-)  C
1349 ASN   ( 500-)  C
1607 HIS   ( 272-)  D
1835 ASN   ( 500-)  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.

   4 ILE   ( 127-)  A      N
   5 HIS   ( 128-)  A      N
   5 HIS   ( 128-)  A      NE2
   8 ASP   ( 131-)  A      N
  13 ILE   ( 136-)  A      N
  15 LYS   ( 138-)  A      N
  17 LEU   ( 140-)  A      N
  20 ASP   ( 143-)  A      N
  23 SER   ( 146-)  A      N
  39 PHE   ( 162-)  A      N
  42 ALA   ( 165-)  A      N
  47 SER   ( 170-)  A      N
  50 THR   ( 173-)  A      N
  51 ARG   ( 174-)  A      NE
  51 ARG   ( 174-)  A      NH1
  51 ARG   ( 174-)  A      NH2
  55 PHE   ( 178-)  A      N
  62 TYR   ( 185-)  A      OH
  76 HIS   ( 199-)  A      N
  79 SER   ( 202-)  A      N
  88 LEU   ( 211-)  A      N
  93 THR   ( 216-)  A      N
  98 PHE   ( 221-)  A      N
 112 ARG   ( 235-)  A      N
 120 THR   ( 243-)  A      OG1
And so on for a total of 315 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.

  36 HIS   ( 159-)  A      ND1
  80 HIS   ( 203-)  A      ND1
 278 GLU   ( 401-)  A      OE2
 491 HIS   ( 128-)  B      NE2
 507 ASP   ( 144-)  B      OD1
 566 HIS   ( 203-)  B      ND1
 980 ASP   ( 131-)  C      OD1
1033 HIS   ( 184-)  C      NE2
1121 HIS   ( 272-)  C      ND1
1349 ASN   ( 500-)  C      OD1
1463 HIS   ( 128-)  D      ND1
1479 ASP   ( 144-)  D      OD1
1494 HIS   ( 159-)  D      ND1
1519 HIS   ( 184-)  D      ND1
1524 HIS   ( 189-)  D      ND1
1525 ASN   ( 190-)  D      OD1
1538 HIS   ( 203-)  D      ND1
1583 ASP   ( 248-)  D      OD2
1903 ASP   ( 568-)  D      OD1

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.

  56 ASP   ( 179-)  A   H-bonding suggests Asn
 138 ASP   ( 261-)  A   H-bonding suggests Asn
 170 GLU   ( 293-)  A   H-bonding suggests Gln; but Alt-Rotamer
 371 ASP   ( 494-)  A   H-bonding suggests Asn
 384 ASP   ( 507-)  A   H-bonding suggests Asn
 455 GLU   ( 584-)  A   H-bonding suggests Gln
 468 ASP   ( 597-)  A   H-bonding suggests Asn
 521 GLU   ( 158-)  B   H-bonding suggests Gln
 593 ASP   ( 230-)  B   H-bonding suggests Asn
 870 ASP   ( 507-)  B   H-bonding suggests Asn; but Alt-Rotamer
 927 GLU   ( 564-)  B   H-bonding suggests Gln
 960 GLU   ( 603-)  B   H-bonding suggests Gln; but Alt-Rotamer
1007 GLU   ( 158-)  C   H-bonding suggests Gln
1110 ASP   ( 261-)  C   H-bonding suggests Asn
1142 GLU   ( 293-)  C   H-bonding suggests Gln
1321 ASP   ( 472-)  C   H-bonding suggests Asn; but Alt-Rotamer
1356 ASP   ( 507-)  C   H-bonding suggests Asn; but Alt-Rotamer
1427 GLU   ( 584-)  C   H-bonding suggests Gln
1514 ASP   ( 179-)  D   H-bonding suggests Asn
1596 ASP   ( 261-)  D   H-bonding suggests Asn
1842 ASP   ( 507-)  D   H-bonding suggests Asn; but Alt-Rotamer
1913 GLU   ( 584-)  D   H-bonding suggests Gln; but Alt-Rotamer

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 :  -1.535
  2nd generation packing quality :  -2.746
  Ramachandran plot appearance   :  -2.524
  chi-1/chi-2 rotamer normality  :  -4.095 (bad)
  Backbone conformation          :  -0.886

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.295 (tight)
  Bond angles                    :   0.560 (tight)
  Omega angle restraints         :   1.172
  Side chain planarity           :   0.245 (tight)
  Improper dihedral distribution :   0.609
  B-factor distribution          :   0.660
  Inside/Outside distribution    :   1.043

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 : 3.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.295 (tight)
  Bond angles                    :   0.560 (tight)
  Omega angle restraints         :   1.172
  Side chain planarity           :   0.245 (tight)
  Improper dihedral distribution :   0.609
  B-factor distribution          :   0.660
  Inside/Outside distribution    :   1.043
==============

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.