WHAT IF Check report

This file was created 2012-01-30 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 pdb3o3c.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 : 0.045
CA-only RMS fit for the two chains : 0.031

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 D

All-atom RMS fit for the two chains : 0.065
CA-only RMS fit for the two chains : 0.048

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 : 0.059
CA-only RMS fit for the two chains : 0.044

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 backbone difference plot

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

Chain identifiers of the two chains: B and D

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2450 UDP   ( 901-)  B  -
2454 UDP   ( 901-)  C  -
2457 UDP   ( 901-)  D  -
2459 UDP   ( 901-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: B-factors outside the range 0.0 - 100.0

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

   1 SER   (   2-)  A    High
   2 ARG   (   3-)  A    High
   3 ASP   (   4-)  A    High
   4 LEU   (   5-)  A    High
   5 GLN   (   6-)  A    High
   6 ASN   (   7-)  A    High
   7 HIS   (   8-)  A    High
  15 GLU   (  16-)  A    High
  19 ARG   (  20-)  A    High
  21 GLY   (  22-)  A    High
  33 ILE   (  34-)  A    High
  39 LYS   (  40-)  A    High
  40 ASP   (  41-)  A    High
  41 HIS   (  42-)  A    High
  51 ALA   (  52-)  A    High
  52 THR   (  53-)  A    High
  54 GLN   (  55-)  A    High
  55 ASN   (  56-)  A    High
  56 GLU   (  57-)  A    High
  58 ASP   (  59-)  A    High
  61 ASP   (  62-)  A    High
  62 TRP   (  63-)  A    High
  63 LYS   (  64-)  A    High
  64 LYS   (  65-)  A    High
  65 PRO   (  66-)  A    High
And so on for a total of 1519 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

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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

  24 TYR   (  25-)  A
  53 TYR   (  54-)  A
 199 TYR   ( 200-)  A
 313 TYR   ( 323-)  A
 330 TYR   ( 340-)  A
 490 TYR   ( 513-)  A
 524 TYR   ( 552-)  A
 543 TYR   ( 571-)  A
 578 TYR   ( 606-)  A
 590 TYR   ( 618-)  A
 635 TYR   (  25-)  B
 664 TYR   (  54-)  B
 924 TYR   ( 323-)  B
 941 TYR   ( 340-)  B
1101 TYR   ( 513-)  B
1135 TYR   ( 552-)  B
1154 TYR   ( 571-)  B
1189 TYR   ( 606-)  B
1201 TYR   ( 618-)  B
1246 TYR   (  25-)  C
1275 TYR   (  54-)  C
1421 TYR   ( 200-)  C
1535 TYR   ( 323-)  C
1552 TYR   ( 340-)  C
1712 TYR   ( 513-)  C
1746 TYR   ( 552-)  C
1765 TYR   ( 571-)  C
1800 TYR   ( 606-)  C
1812 TYR   ( 618-)  C
1857 TYR   (  25-)  D
1886 TYR   (  54-)  D
2032 TYR   ( 200-)  D
2146 TYR   ( 323-)  D
2163 TYR   ( 340-)  D
2323 TYR   ( 513-)  D
2357 TYR   ( 552-)  D
2376 TYR   ( 571-)  D
2411 TYR   ( 606-)  D
2423 TYR   ( 618-)  D

Warning: Phenylalanine convention problem

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

  68 PHE   (  69-)  A
  89 PHE   (  90-)  A
 166 PHE   ( 167-)  A
 206 PHE   ( 209-)  A
 250 PHE   ( 253-)  A
 291 PHE   ( 301-)  A
 297 PHE   ( 307-)  A
 306 PHE   ( 316-)  A
 344 PHE   ( 354-)  A
 384 PHE   ( 394-)  A
 594 PHE   ( 622-)  A
 679 PHE   (  69-)  B
 700 PHE   (  90-)  B
 777 PHE   ( 167-)  B
 817 PHE   ( 209-)  B
 861 PHE   ( 253-)  B
 902 PHE   ( 301-)  B
 917 PHE   ( 316-)  B
 955 PHE   ( 354-)  B
 995 PHE   ( 394-)  B
1205 PHE   ( 622-)  B
1290 PHE   (  69-)  C
1311 PHE   (  90-)  C
1388 PHE   ( 167-)  C
1428 PHE   ( 209-)  C
1472 PHE   ( 253-)  C
1495 PHE   ( 276-)  C
1513 PHE   ( 301-)  C
1519 PHE   ( 307-)  C
1528 PHE   ( 316-)  C
1566 PHE   ( 354-)  C
1606 PHE   ( 394-)  C
1816 PHE   ( 622-)  C
1901 PHE   (  69-)  D
1999 PHE   ( 167-)  D
2039 PHE   ( 209-)  D
2083 PHE   ( 253-)  D
2124 PHE   ( 301-)  D
2130 PHE   ( 307-)  D
2139 PHE   ( 316-)  D
2177 PHE   ( 354-)  D
2217 PHE   ( 394-)  D
2427 PHE   ( 622-)  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.

 214 ASP   ( 217-)  A
 216 ASP   ( 219-)  A
 298 ASP   ( 308-)  A
 319 ASP   ( 329-)  A
 385 ASP   ( 395-)  A
 567 ASP   ( 595-)  A
 604 ASP   ( 632-)  A
 825 ASP   ( 217-)  B
 827 ASP   ( 219-)  B
 909 ASP   ( 308-)  B
 930 ASP   ( 329-)  B
 996 ASP   ( 395-)  B
1178 ASP   ( 595-)  B
1215 ASP   ( 632-)  B
1436 ASP   ( 217-)  C
1438 ASP   ( 219-)  C
1520 ASP   ( 308-)  C
1541 ASP   ( 329-)  C
1607 ASP   ( 395-)  C
1789 ASP   ( 595-)  C
1826 ASP   ( 632-)  C
2047 ASP   ( 217-)  D
2049 ASP   ( 219-)  D
2131 ASP   ( 308-)  D
2152 ASP   ( 329-)  D
2218 ASP   ( 395-)  D
2400 ASP   ( 595-)  D
2437 ASP   ( 632-)  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.

  15 GLU   (  16-)  A
  71 GLU   (  72-)  A
  83 GLU   (  84-)  A
  97 GLU   (  98-)  A
 116 GLU   ( 117-)  A
 131 GLU   ( 132-)  A
 168 GLU   ( 169-)  A
 211 GLU   ( 214-)  A
 218 GLU   ( 221-)  A
 231 GLU   ( 234-)  A
 251 GLU   ( 254-)  A
 253 GLU   ( 256-)  A
 357 GLU   ( 367-)  A
 456 GLU   ( 479-)  A
 494 GLU   ( 517-)  A
 577 GLU   ( 605-)  A
 600 GLU   ( 628-)  A
 626 GLU   (  16-)  B
 682 GLU   (  72-)  B
 694 GLU   (  84-)  B
 708 GLU   (  98-)  B
 727 GLU   ( 117-)  B
 742 GLU   ( 132-)  B
 779 GLU   ( 169-)  B
 822 GLU   ( 214-)  B
And so on for a total of 68 lines.

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.

 477 HIS   ( 500-)  A      CG   ND1  CE1 109.63    4.0
1389 HIS   ( 168-)  C      CG   ND1  CE1 109.81    4.2
1497 LEU   ( 285-)  C      N    CA   C   124.61    4.8
1699 HIS   ( 500-)  C      CG   ND1  CE1 109.65    4.1

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.

  15 GLU   (  16-)  A
  71 GLU   (  72-)  A
  83 GLU   (  84-)  A
  97 GLU   (  98-)  A
 116 GLU   ( 117-)  A
 131 GLU   ( 132-)  A
 168 GLU   ( 169-)  A
 211 GLU   ( 214-)  A
 214 ASP   ( 217-)  A
 216 ASP   ( 219-)  A
 218 GLU   ( 221-)  A
 231 GLU   ( 234-)  A
 251 GLU   ( 254-)  A
 253 GLU   ( 256-)  A
 298 ASP   ( 308-)  A
 319 ASP   ( 329-)  A
 357 GLU   ( 367-)  A
 385 ASP   ( 395-)  A
 456 GLU   ( 479-)  A
 494 GLU   ( 517-)  A
 567 ASP   ( 595-)  A
 577 GLU   ( 605-)  A
 600 GLU   ( 628-)  A
 604 ASP   ( 632-)  A
 626 GLU   (  16-)  B
And so on for a total of 96 lines.

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.

1497 LEU   ( 285-)  C    5.41
2108 LEU   ( 285-)  D    4.36

Error: Side chain planarity problems

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

1389 HIS   ( 168-)  C    4.17

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.560

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.

2015 ARG   ( 183-)  D    -2.9
 793 ARG   ( 183-)  B    -2.9
1404 ARG   ( 183-)  C    -2.9
 182 ARG   ( 183-)  A    -2.8
1634 PRO   ( 435-)  C    -2.8
2245 PRO   ( 435-)  D    -2.8
1261 LYS   (  40-)  C    -2.8
1872 LYS   (  40-)  D    -2.8
  39 LYS   (  40-)  A    -2.8
 650 LYS   (  40-)  B    -2.8
1023 PRO   ( 435-)  B    -2.8
  16 VAL   (  17-)  A    -2.7
1238 VAL   (  17-)  C    -2.7
 627 VAL   (  17-)  B    -2.7
1849 VAL   (  17-)  D    -2.7
 412 PRO   ( 435-)  A    -2.7
1075 ILE   ( 487-)  B    -2.7
 464 ILE   ( 487-)  A    -2.7
2297 ILE   ( 487-)  D    -2.6
1686 ILE   ( 487-)  C    -2.6
1332 VAL   ( 111-)  C    -2.6
1943 VAL   ( 111-)  D    -2.6
 110 VAL   ( 111-)  A    -2.5
 721 VAL   ( 111-)  B    -2.5
 964 SER   ( 363-)  B    -2.5
And so on for a total of 90 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.

  16 VAL   (  17-)  A  Poor phi/psi
  20 VAL   (  21-)  A  Poor phi/psi
  39 LYS   (  40-)  A  Poor phi/psi
  52 THR   (  53-)  A  Poor phi/psi
  95 LEU   (  96-)  A  Poor phi/psi
 101 LYS   ( 102-)  A  omega poor
 110 VAL   ( 111-)  A  Poor phi/psi
 113 TYR   ( 114-)  A  Poor phi/psi
 124 LEU   ( 125-)  A  Poor phi/psi
 160 HIS   ( 161-)  A  omega poor
 168 GLU   ( 169-)  A  Poor phi/psi
 193 ALA   ( 194-)  A  Poor phi/psi
 206 PHE   ( 209-)  A  Poor phi/psi, omega poor
 208 ASN   ( 211-)  A  Poor phi/psi
 257 LYS   ( 260-)  A  Poor phi/psi
 335 SER   ( 345-)  A  Poor phi/psi
 336 GLY   ( 346-)  A  Poor phi/psi
 353 SER   ( 363-)  A  Poor phi/psi
 361 GLY   ( 371-)  A  Poor phi/psi
 390 TYR   ( 400-)  A  PRO omega poor
 426 ASP   ( 449-)  A  Poor phi/psi
 440 GLN   ( 463-)  A  Poor phi/psi
 443 ASN   ( 466-)  A  Poor phi/psi
 455 PRO   ( 478-)  A  Poor phi/psi
 465 LEU   ( 488-)  A  omega poor
And so on for a total of 106 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.880

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.

1008 SER   ( 420-)  B    0.35
1619 SER   ( 420-)  C    0.37
 397 SER   ( 420-)  A    0.37
1174 GLU   ( 591-)  B    0.38
 378 SER   ( 388-)  A    0.38
1785 GLU   ( 591-)  C    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!

   6 ASN   (   7-)  A      0
  13 ALA   (  14-)  A      0
  16 VAL   (  17-)  A      0
  17 ALA   (  18-)  A      0
  18 ASN   (  19-)  A      0
  19 ARG   (  20-)  A      0
  39 LYS   (  40-)  A      0
  40 ASP   (  41-)  A      0
  41 HIS   (  42-)  A      0
  45 ILE   (  46-)  A      0
  52 THR   (  53-)  A      0
  67 ALA   (  68-)  A      0
  72 MET   (  73-)  A      0
  91 TYR   (  92-)  A      0
  95 LEU   (  96-)  A      0
  96 ILE   (  97-)  A      0
  97 GLU   (  98-)  A      0
 110 VAL   ( 111-)  A      0
 123 SER   ( 124-)  A      0
 124 LEU   ( 125-)  A      0
 125 VAL   ( 126-)  A      0
 132 ASN   ( 133-)  A      0
 156 LEU   ( 157-)  A      0
 158 SER   ( 159-)  A      0
 159 GLN   ( 160-)  A      0
And so on for a total of 748 lines.

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]

 100 PRO   ( 101-)  A    0.46 HIGH
 711 PRO   ( 101-)  B    0.47 HIGH
1322 PRO   ( 101-)  C    0.46 HIGH
1933 PRO   ( 101-)  D    0.46 HIGH

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].

 176 PRO   ( 177-)  A   101.6 envelop C-beta (108 degrees)
 348 PRO   ( 358-)  A    26.8 half-chair N/C-delta (18 degrees)
 412 PRO   ( 435-)  A   130.0 half-chair C-beta/C-alpha (126 degrees)
 482 PRO   ( 505-)  A    48.1 half-chair C-delta/C-gamma (54 degrees)
 492 PRO   ( 515-)  A  -113.7 envelop C-gamma (-108 degrees)
 787 PRO   ( 177-)  B   102.2 envelop C-beta (108 degrees)
 959 PRO   ( 358-)  B    25.4 half-chair N/C-delta (18 degrees)
1023 PRO   ( 435-)  B   129.7 half-chair C-beta/C-alpha (126 degrees)
1093 PRO   ( 505-)  B    48.7 half-chair C-delta/C-gamma (54 degrees)
1103 PRO   ( 515-)  B  -113.8 envelop C-gamma (-108 degrees)
1570 PRO   ( 358-)  C    28.0 envelop C-delta (36 degrees)
1634 PRO   ( 435-)  C   127.3 half-chair C-beta/C-alpha (126 degrees)
1704 PRO   ( 505-)  C    50.3 half-chair C-delta/C-gamma (54 degrees)
1714 PRO   ( 515-)  C  -112.3 envelop C-gamma (-108 degrees)
2181 PRO   ( 358-)  D    28.1 envelop C-delta (36 degrees)
2245 PRO   ( 435-)  D   127.7 half-chair C-beta/C-alpha (126 degrees)
2315 PRO   ( 505-)  D    48.5 half-chair C-delta/C-gamma (54 degrees)
2325 PRO   ( 515-)  D  -112.4 envelop C-gamma (-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.

1000 ARG   ( 399-)  B      NH2 <-> 2130 PHE   ( 307-)  D      O      0.60    2.10  INTRA BF
 908 PHE   ( 307-)  B      O   <-> 2222 ARG   ( 399-)  D      NH2    0.40    2.30  INTRA BF
1120 GLY   ( 532-)  B      O   <-> 1123 SER   ( 535-)  B      OG     0.37    2.03  INTRA BL
2342 GLY   ( 532-)  D      O   <-> 2345 SER   ( 535-)  D      OG     0.37    2.03  INTRA BL
   2 ARG   (   3-)  A      NH1 <->  184 ASP   ( 185-)  A      OD2    0.36    2.34  INTRA BF
 613 ARG   (   3-)  B      NH1 <->  795 ASP   ( 185-)  B      OD2    0.35    2.35  INTRA BF
1871 TYR   (  39-)  D      OH  <-> 2415 ARG   ( 610-)  D      NH1    0.35    2.35  INTRA BL
1224 ARG   (   3-)  C      NH1 <-> 1406 ASP   ( 185-)  C      OD2    0.34    2.36  INTRA BL
 509 GLY   ( 532-)  A      O   <->  512 SER   ( 535-)  A      OG     0.34    2.06  INTRA BL
1731 GLY   ( 532-)  C      O   <-> 1734 SER   ( 535-)  C      OG     0.34    2.06  INTRA BL
  73 ARG   (  74-)  A      NH1 <->   76 GLN   (  77-)  A      OE1    0.34    2.36  INTRA BF
1835 ARG   (   3-)  D      NH1 <-> 2017 ASP   ( 185-)  D      OD2    0.33    2.37  INTRA BL
 649 TYR   (  39-)  B      OH  <-> 1193 ARG   ( 610-)  B      NH1    0.33    2.37  INTRA BL
 684 ARG   (  74-)  B      NH1 <->  687 GLN   (  77-)  B      OE1    0.32    2.38  INTRA BF
1852 ARG   (  20-)  D      NH1 <-> 2456 SO4   ( 801-)  D      O3     0.32    2.38  INTRA BF
1906 ARG   (  74-)  D      NH1 <-> 1909 GLN   (  77-)  D      OE1    0.31    2.39  INTRA BL
2109 HIS   ( 286-)  D      ND1 <-> 2392 ARG   ( 587-)  D      NH2    0.31    2.69  INTRA BL
  38 TYR   (  39-)  A      OH  <->  582 ARG   ( 610-)  A      NH1    0.31    2.39  INTRA BL
1295 ARG   (  74-)  C      NH1 <-> 1298 GLN   (  77-)  C      OE1    0.31    2.39  INTRA BF
1498 HIS   ( 286-)  C      ND1 <-> 1781 ARG   ( 587-)  C      NH2    0.30    2.70  INTRA BF
 887 HIS   ( 286-)  B      ND1 <-> 1170 ARG   ( 587-)  B      NH2    0.30    2.70  INTRA BF
 276 HIS   ( 286-)  A      ND1 <->  559 ARG   ( 587-)  A      NH2    0.30    2.70  INTRA BL
 389 ARG   ( 399-)  A      NH2 <-> 1519 PHE   ( 307-)  C      O      0.30    2.40  INTRA BF
  95 LEU   (  96-)  A      CD1 <-> 2240 LEU   ( 430-)  D      CD1    0.29    2.91  INTRA BL
 719 ASP   ( 109-)  B      OD1 <->  722 ARG   ( 112-)  B      NH1    0.27    2.43  INTRA BF
And so on for a total of 374 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.

1241 ARG   (  20-)  C      -7.30
 630 ARG   (  20-)  B      -7.30
  19 ARG   (  20-)  A      -7.29
1852 ARG   (  20-)  D      -7.25
 415 GLN   ( 438-)  A      -6.42
1026 GLN   ( 438-)  B      -6.41
1637 GLN   ( 438-)  C      -6.41
2248 GLN   ( 438-)  D      -6.38
1021 ARG   ( 433-)  B      -6.15
 410 ARG   ( 433-)  A      -6.10
1632 ARG   ( 433-)  C      -6.03
1633 ARG   ( 434-)  C      -6.02
1022 ARG   ( 434-)  B      -5.99
 411 ARG   ( 434-)  A      -5.93
2244 ARG   ( 434-)  D      -5.86
2243 ARG   ( 433-)  D      -5.80
 921 ARG   ( 320-)  B      -5.63
1611 ARG   ( 399-)  C      -5.57
2054 ARG   ( 224-)  D      -5.51
 832 ARG   ( 224-)  B      -5.51
1443 ARG   ( 224-)  C      -5.51
 221 ARG   ( 224-)  A      -5.50
2223 TYR   ( 400-)  D      -5.48
1532 ARG   ( 320-)  C      -5.43
2143 ARG   ( 320-)  D      -5.42
2222 ARG   ( 399-)  D      -5.42
 389 ARG   ( 399-)  A      -5.41
1560 LYS   ( 348-)  C      -5.40
2171 LYS   ( 348-)  D      -5.38
1000 ARG   ( 399-)  B      -5.36
1001 TYR   ( 400-)  B      -5.34
1068 PHE   ( 480-)  B      -5.34
 457 PHE   ( 480-)  A      -5.31
1679 PHE   ( 480-)  C      -5.31
 416 LEU   ( 439-)  A      -5.25
 949 LYS   ( 348-)  B      -5.25
1027 LEU   ( 439-)  B      -5.25
1638 LEU   ( 439-)  C      -5.23
2290 PHE   ( 480-)  D      -5.23
 338 LYS   ( 348-)  A      -5.20
2249 LEU   ( 439-)  D      -5.18
 310 ARG   ( 320-)  A      -5.17
1263 HIS   (  42-)  C      -5.01

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.

1630 ALA   ( 431-)  C   -2.78
2241 ALA   ( 431-)  D   -2.76
2242 LEU   ( 432-)  D   -2.57
1020 LEU   ( 432-)  B   -2.54
1631 LEU   ( 432-)  C   -2.51
 409 LEU   ( 432-)  A   -2.51

Warning: Abnormal packing Z-score for sequential residues

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

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

 200 LEU   ( 201-)  A     -  203 SER   ( 204-)  A        -1.53
 811 LEU   ( 201-)  B     -  814 SER   ( 204-)  B        -1.49
1422 LEU   ( 201-)  C     - 1425 SER   ( 204-)  C        -1.54
2033 LEU   ( 201-)  D     - 2036 SER   ( 204-)  D        -1.52

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.

   7 HIS   (   8-)  A
  77 HIS   (  78-)  A
 132 ASN   ( 133-)  A
 167 HIS   ( 168-)  A
 236 HIS   ( 239-)  A
 290 HIS   ( 300-)  A
 461 ASN   ( 484-)  A
 477 HIS   ( 500-)  A
 606 ASN   ( 634-)  A
 618 HIS   (   8-)  B
 688 HIS   (  78-)  B
 743 ASN   ( 133-)  B
 778 HIS   ( 168-)  B
 901 HIS   ( 300-)  B
1072 ASN   ( 484-)  B
1088 HIS   ( 500-)  B
1217 ASN   ( 634-)  B
1229 HIS   (   8-)  C
1389 HIS   ( 168-)  C
1512 HIS   ( 300-)  C
1683 ASN   ( 484-)  C
1699 HIS   ( 500-)  C
1828 ASN   ( 634-)  C
1840 HIS   (   8-)  D
2000 HIS   ( 168-)  D
2123 HIS   ( 300-)  D
2294 ASN   ( 484-)  D
2310 HIS   ( 500-)  D
2439 ASN   ( 634-)  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.

   2 ARG   (   3-)  A      N
   6 ASN   (   7-)  A      N
  17 ALA   (  18-)  A      N
  21 GLY   (  22-)  A      N
  24 TYR   (  25-)  A      N
  43 HIS   (  44-)  A      ND1
  54 GLN   (  55-)  A      N
  62 TRP   (  63-)  A      N
  80 GLN   (  81-)  A      NE2
 110 VAL   ( 111-)  A      N
 115 ASN   ( 116-)  A      N
 127 ILE   ( 128-)  A      N
 162 ILE   ( 163-)  A      N
 169 TRP   ( 170-)  A      N
 170 LEU   ( 171-)  A      N
 173 VAL   ( 174-)  A      N
 174 ALA   ( 175-)  A      N
 177 LEU   ( 178-)  A      N
 193 ALA   ( 194-)  A      N
 207 TYR   ( 210-)  A      N
 208 ASN   ( 211-)  A      N
 212 SER   ( 215-)  A      N
 216 ASP   ( 219-)  A      N
 245 SER   ( 248-)  A      N
 258 ARG   ( 261-)  A      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.

   7 HIS   (   8-)  A      NE2
 165 HIS   ( 166-)  A      ND1
 216 ASP   ( 219-)  A      OD1
 266 ASN   ( 269-)  A      OD1
 315 ASN   ( 325-)  A      OD1
 454 HIS   ( 477-)  A      NE2
 558 GLN   ( 586-)  A      OE1
 618 HIS   (   8-)  B      NE2
 776 HIS   ( 166-)  B      ND1
 842 GLU   ( 234-)  B      OE2
 877 ASN   ( 269-)  B      OD1
 926 ASN   ( 325-)  B      OD1
1065 HIS   ( 477-)  B      NE2
1377 HIS   ( 156-)  C      ND1
1387 HIS   ( 166-)  C      ND1
1438 ASP   ( 219-)  C      OD1
1488 ASN   ( 269-)  C      OD1
1676 HIS   ( 477-)  C      NE2
1840 HIS   (   8-)  D      NE2
1988 HIS   ( 156-)  D      ND1
1998 HIS   ( 166-)  D      ND1
2049 ASP   ( 219-)  D      OD1
2064 GLU   ( 234-)  D      OE2
2099 ASN   ( 269-)  D      OD1
2148 ASN   ( 325-)  D      OD1
2287 HIS   ( 477-)  D      NE2

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.

 138 ASP   ( 139-)  A   H-bonding suggests Asn
 392 GLU   ( 415-)  A   H-bonding suggests Gln
 542 ASP   ( 570-)  A   H-bonding suggests Asn
 570 ASP   ( 598-)  A   H-bonding suggests Asn; but Alt-Rotamer
 749 ASP   ( 139-)  B   H-bonding suggests Asn
1003 GLU   ( 415-)  B   H-bonding suggests Gln
1127 ASP   ( 539-)  B   H-bonding suggests Asn
1153 ASP   ( 570-)  B   H-bonding suggests Asn
1181 ASP   ( 598-)  B   H-bonding suggests Asn; but Alt-Rotamer
1360 ASP   ( 139-)  C   H-bonding suggests Asn
1614 GLU   ( 415-)  C   H-bonding suggests Gln
1764 ASP   ( 570-)  C   H-bonding suggests Asn
1792 ASP   ( 598-)  C   H-bonding suggests Asn; but Alt-Rotamer
2225 GLU   ( 415-)  D   H-bonding suggests Gln
2375 ASP   ( 570-)  D   H-bonding suggests Asn
2403 ASP   ( 598-)  D   H-bonding suggests Asn; 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 :  -0.369
  2nd generation packing quality :  -1.087
  Ramachandran plot appearance   :  -3.560 (poor)
  chi-1/chi-2 rotamer normality  :  -3.880 (poor)
  Backbone conformation          :  -0.028

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.616 (tight)
  Omega angle restraints         :   0.986
  Side chain planarity           :   0.311 (tight)
  Improper dihedral distribution :   0.618
  B-factor distribution          :   0.532
  Inside/Outside distribution    :   1.020

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 : 3.51


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :   0.9
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.616 (tight)
  Omega angle restraints         :   0.986
  Side chain planarity           :   0.311 (tight)
  Improper dihedral distribution :   0.618
  B-factor distribution          :   0.532
  Inside/Outside distribution    :   1.020
==============

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.