WHAT IF Check report

This file was created 2012-04-04 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 pdb2zky.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 : 0.634
CA-only RMS fit for the two chains : 0.274

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 : 0.747
CA-only RMS fit for the two chains : 0.316

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 : 0.701
CA-only RMS fit for the two chains : 0.260

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.651
CA-only RMS fit for the two chains : 0.244

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.637
CA-only RMS fit for the two chains : 0.262

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and F

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: 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.

  76 GLU   (  77-)  A    High
 131 GLU   ( 132-)  A    High
 381 GLU   (  77-)  C    High
 414 HIS   ( 110-)  C    High
 939 LYS   (  23-)  G    High
 940 GLU   (  24-)  G    High
 941 SER   (  25-)  G    High
 942 ASN   (  26-)  G    High
 985 ARG   (  69-)  G    High
 993 GLU   (  77-)  G    High
 994 GLU   (  78-)  G    High
1025 ASP   ( 109-)  G    High
1047 ASN   ( 131-)  G    High
1048 GLU   ( 132-)  G    High
1222 GLN   ( 153-)  H    High
1246 GLU   (  24-)  I    High
1247 SER   (  25-)  I    High
1248 ASN   (  26-)  I    High
1291 ARG   (  69-)  I    High
1299 GLU   (  77-)  I    High
1352 GLY   ( 130-)  I    High
1353 ASN   ( 131-)  I    High
1354 GLU   ( 132-)  I    High
1358 LYS   ( 136-)  I    High
1399 GLU   (  24-)  J    High
1401 ASN   (  26-)  J    High
1452 GLU   (  77-)  J    High

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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.

  78 ARG   (  79-)  A
 114 ARG   ( 115-)  A
 142 ARG   ( 143-)  A
 266 ARG   ( 115-)  B
 294 ARG   ( 143-)  B
 447 ARG   ( 143-)  C
 572 ARG   ( 115-)  D
 600 ARG   ( 143-)  D
 725 ARG   ( 115-)  E
 753 ARG   ( 143-)  E
 906 ARG   ( 143-)  F
1031 ARG   ( 115-)  G
1059 ARG   ( 143-)  G
1212 ARG   ( 143-)  H
1337 ARG   ( 115-)  I
1365 ARG   ( 143-)  I
1518 ARG   ( 143-)  J

Warning: Phenylalanine convention problem

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

  19 PHE   (  20-)  A
  63 PHE   (  64-)  A
 171 PHE   (  20-)  B
 215 PHE   (  64-)  B
 324 PHE   (  20-)  C
 368 PHE   (  64-)  C
 521 PHE   (  64-)  D
 630 PHE   (  20-)  E
 674 PHE   (  64-)  E
 783 PHE   (  20-)  F
 827 PHE   (  64-)  F
 936 PHE   (  20-)  G
 980 PHE   (  64-)  G
1089 PHE   (  20-)  H
1133 PHE   (  64-)  H
1242 PHE   (  20-)  I
1286 PHE   (  64-)  I
1395 PHE   (  20-)  J
1439 PHE   (  64-)  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.

  10 ASP   (  11-)  A
  51 ASP   (  52-)  A
  75 ASP   (  76-)  A
  89 ASP   (  90-)  A
  91 ASP   (  92-)  A
 100 ASP   ( 101-)  A
 123 ASP   ( 124-)  A
 124 ASP   ( 125-)  A
 162 ASP   (  11-)  B
 203 ASP   (  52-)  B
 227 ASP   (  76-)  B
 241 ASP   (  90-)  B
 243 ASP   (  92-)  B
 247 ASP   (  96-)  B
 252 ASP   ( 101-)  B
 275 ASP   ( 124-)  B
 276 ASP   ( 125-)  B
 315 ASP   (  11-)  C
 356 ASP   (  52-)  C
 380 ASP   (  76-)  C
 394 ASP   (  90-)  C
 396 ASP   (  92-)  C
 400 ASP   (  96-)  C
 405 ASP   ( 101-)  C
 428 ASP   ( 124-)  C
And so on for a total of 74 lines.

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.

  39 GLU   (  40-)  A
  48 GLU   (  49-)  A
  77 GLU   (  78-)  A
 120 GLU   ( 121-)  A
 132 GLU   ( 133-)  A
 172 GLU   (  21-)  B
 191 GLU   (  40-)  B
 200 GLU   (  49-)  B
 229 GLU   (  78-)  B
 251 GLU   ( 100-)  B
 272 GLU   ( 121-)  B
 284 GLU   ( 133-)  B
 325 GLU   (  21-)  C
 353 GLU   (  49-)  C
 425 GLU   ( 121-)  C
 437 GLU   ( 133-)  C
 478 GLU   (  21-)  D
 481 GLU   (  24-)  D
 497 GLU   (  40-)  D
 506 GLU   (  49-)  D
 535 GLU   (  78-)  D
 578 GLU   ( 121-)  D
 589 GLU   ( 132-)  D
 590 GLU   ( 133-)  D
 634 GLU   (  24-)  E
And so on for a total of 52 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.

 200 GLU   (  49-)  B      N    CA   C   123.66    4.5
 238 VAL   (  87-)  B      N    CA   C    99.86   -4.0
 367 HIS   (  63-)  C      CG   ND1  CE1 109.67    4.1
 659 GLU   (  49-)  E      N    CA   C   122.60    4.1
 996 HIS   (  80-)  G      CG   ND1  CE1 109.64    4.0
1156 VAL   (  87-)  H      N    CA   C    98.86   -4.4
1309 VAL   (  87-)  I      N    CA   C    97.84   -4.8
1424 GLU   (  49-)  J      N    CA   C   122.56    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.

  10 ASP   (  11-)  A
  39 GLU   (  40-)  A
  48 GLU   (  49-)  A
  51 ASP   (  52-)  A
  75 ASP   (  76-)  A
  77 GLU   (  78-)  A
  78 ARG   (  79-)  A
  89 ASP   (  90-)  A
  91 ASP   (  92-)  A
 100 ASP   ( 101-)  A
 114 ARG   ( 115-)  A
 120 GLU   ( 121-)  A
 123 ASP   ( 124-)  A
 124 ASP   ( 125-)  A
 132 GLU   ( 133-)  A
 142 ARG   ( 143-)  A
 162 ASP   (  11-)  B
 172 GLU   (  21-)  B
 191 GLU   (  40-)  B
 200 GLU   (  49-)  B
 203 ASP   (  52-)  B
 227 ASP   (  76-)  B
 229 GLU   (  78-)  B
 241 ASP   (  90-)  B
 243 ASP   (  92-)  B
And so on for a total of 143 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.

1309 VAL   (  87-)  I    4.96
1156 VAL   (  87-)  H    4.50
 577 HIS   ( 120-)  D    4.28
1189 HIS   ( 120-)  H    4.27
 883 HIS   ( 120-)  F    4.23
1342 HIS   ( 120-)  I    4.22
 200 GLU   (  49-)  B    4.17
 389 GLY   (  85-)  C    4.08
 730 HIS   ( 120-)  E    4.06
 238 VAL   (  87-)  B    4.04
1268 HIS   (  46-)  I    4.03

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.

 929 PRO   (  13-)  G    -2.7
1284 PRO   (  62-)  I    -2.7
  68 ARG   (  69-)  A    -2.6
 383 ARG   (  79-)  C    -2.5
 230 ARG   (  79-)  B    -2.4
1184 ARG   ( 115-)  H    -2.4
 776 PRO   (  13-)  F    -2.3
 164 PRO   (  13-)  B    -2.3
 526 ARG   (  69-)  D    -2.3
 462 VAL   (   5-)  D    -2.3
 536 ARG   (  79-)  D    -2.3
1148 ARG   (  79-)  H    -2.3
1380 VAL   (   5-)  J    -2.3
1454 ARG   (  79-)  J    -2.3
 768 VAL   (   5-)  F    -2.3
 358 THR   (  54-)  C    -2.2
 156 VAL   (   5-)  B    -2.2
1204 THR   ( 135-)  H    -2.2
 842 ARG   (  79-)  F    -2.2
 689 ARG   (  79-)  E    -2.2
1443 SER   (  68-)  J    -2.2
1301 ARG   (  79-)  I    -2.2
1074 VAL   (   5-)  H    -2.2
1195 LEU   ( 126-)  H    -2.2
1290 SER   (  68-)  I    -2.2
 419 ARG   ( 115-)  C    -2.2
 921 VAL   (   5-)  G    -2.2
 961 PHE   (  45-)  G    -2.2
 213 PRO   (  62-)  B    -2.2
 372 SER   (  68-)  C    -2.2
   4 VAL   (   5-)  A    -2.1
 309 VAL   (   5-)  C    -2.1
1227 VAL   (   5-)  I    -2.1
1400 SER   (  25-)  J    -2.1
1014 SER   (  98-)  G    -2.1
 615 VAL   (   5-)  E    -2.1
 382 GLU   (  78-)  C    -2.1
 402 SER   (  98-)  C    -2.1
 623 PRO   (  13-)  E    -2.1
1267 PHE   (  45-)  I    -2.1
 655 PHE   (  45-)  E    -2.0
 430 LEU   ( 126-)  C    -2.0
 672 PRO   (  62-)  E    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  67 SER   (  68-)  A  Poor phi/psi
  92 ALA   (  93-)  A  Poor phi/psi
 244 ALA   (  93-)  B  Poor phi/psi
 290 ASN   ( 139-)  B  Poor phi/psi
 397 ALA   (  93-)  C  Poor phi/psi
 413 ASP   ( 109-)  C  Poor phi/psi
 430 LEU   ( 126-)  C  Poor phi/psi
 443 ASN   ( 139-)  C  Poor phi/psi
 550 ALA   (  93-)  D  Poor phi/psi
 583 LEU   ( 126-)  D  Poor phi/psi
 596 ASN   ( 139-)  D  Poor phi/psi
 703 ALA   (  93-)  E  Poor phi/psi
 749 ASN   ( 139-)  E  Poor phi/psi
 856 ALA   (  93-)  F  Poor phi/psi
 902 ASN   ( 139-)  F  Poor phi/psi
 984 SER   (  68-)  G  Poor phi/psi
1009 ALA   (  93-)  G  Poor phi/psi
1042 LEU   ( 126-)  G  Poor phi/psi
1044 LYS   ( 128-)  G  Poor phi/psi
1045 GLY   ( 129-)  G  Poor phi/psi
1137 SER   (  68-)  H  Poor phi/psi
1162 ALA   (  93-)  H  Poor phi/psi
1208 ASN   ( 139-)  H  Poor phi/psi
1221 ALA   ( 152-)  H  Poor phi/psi
1290 SER   (  68-)  I  Poor phi/psi
1315 ALA   (  93-)  I  Poor phi/psi
1348 LEU   ( 126-)  I  Poor phi/psi
1361 ASN   ( 139-)  I  Poor phi/psi
1468 ALA   (  93-)  J  Poor phi/psi
1482 SER   ( 107-)  J  Poor phi/psi
1514 ASN   ( 139-)  J  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.992

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.

 285 SER   ( 134-)  B    0.36
 897 SER   ( 134-)  F    0.37

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   (   9-)  A      0
  12 PRO   (  13-)  A      0
  14 GLN   (  15-)  A      0
  22 LYS   (  23-)  A      0
  23 GLU   (  24-)  A      0
  31 TRP   (  32-)  A      0
  35 LYS   (  36-)  A      0
  39 GLU   (  40-)  A      0
  41 LEU   (  42-)  A      0
  45 HIS   (  46-)  A      0
  52 ASN   (  53-)  A      0
  53 THR   (  54-)  A      0
  56 CYS   (  57-)  A      0
  59 ALA   (  60-)  A      0
  61 PRO   (  62-)  A      0
  62 HIS   (  63-)  A      0
  63 PHE   (  64-)  A      0
  64 ASN   (  65-)  A      0
  70 HIS   (  71-)  A      0
  78 ARG   (  79-)  A      0
  83 LEU   (  84-)  A      0
  85 ASN   (  86-)  A      0
 101 SER   ( 102-)  A      0
 102 VAL   ( 103-)  A      0
 103 ILE   ( 104-)  A      0
And so on for a total of 765 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.617

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!

1352 GLY   ( 130-)  I   2.14   14
 412 GLY   ( 108-)  C   1.57   10
 434 GLY   ( 130-)  C   1.55   24
1204 THR   ( 135-)  H   1.51   15

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 271 HIS   ( 120-)  B   1.58
 730 HIS   ( 120-)  E   1.62

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]

 623 PRO   (  13-)  E    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].

 225 PRO   (  74-)  B  -114.2 envelop C-gamma (-108 degrees)
 638 PRO   (  28-)  E    50.1 half-chair C-delta/C-gamma (54 degrees)
1296 PRO   (  74-)  I  -113.1 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.

 412 GLY   ( 108-)  C      O   <->  414 HIS   ( 110-)  C      N      0.42    2.28  INTRA BF
1454 ARG   (  79-)  J      NH2 <-> 1476 ASP   ( 101-)  J      OD1    0.35    2.35  INTRA BF
 842 ARG   (  79-)  F      NH2 <->  864 ASP   ( 101-)  F      OD1    0.35    2.35  INTRA BL
1285 HIS   (  63-)  I      NE2 <-> 1557 HOH   ( 632 )  I      O      0.34    2.36  INTRA BF
1044 LYS   ( 128-)  G      O   <-> 1046 GLY   ( 130-)  G      N      0.26    2.44  INTRA BF
 350 HIS   (  46-)  C      ND1 <->  367 HIS   (  63-)  C      NE2    0.25    2.75  INTRA BF
 230 ARG   (  79-)  B      NH2 <->  252 ASP   ( 101-)  B      OD1    0.24    2.46  INTRA BL
 940 GLU   (  24-)  G      O   <->  942 ASN   (  26-)  G      N      0.24    2.46  INTRA BF
 689 ARG   (  79-)  E      NH2 <->  711 ASP   ( 101-)  E      OD1    0.24    2.46  INTRA BL
 367 HIS   (  63-)  C      NE2 <-> 1551 HOH   ( 632 )  C      O      0.23    2.47  INTRA BF
1148 ARG   (  79-)  H      NH2 <-> 1170 ASP   ( 101-)  H      OD1    0.23    2.47  INTRA BL
 720 HIS   ( 110-)  E      N   <-> 1553 HOH   ( 624 )  E      O      0.23    2.47  INTRA BF
1268 HIS   (  46-)  I      ND1 <-> 1342 HIS   ( 120-)  I      CD2    0.23    2.87  INTRA
1002 ASN   (  86-)  G      OD1 <-> 1040 ASP   ( 124-)  G      N      0.22    2.48  INTRA BF
 556 ILE   (  99-)  D      CG2 <->  557 GLU   ( 100-)  D      N      0.21    2.79  INTRA BL
 383 ARG   (  79-)  C      NH2 <->  405 ASP   ( 101-)  C      OD1    0.21    2.49  INTRA BF
1134 ASN   (  65-)  H      N   <-> 1556 HOH   ( 641 )  H      O      0.20    2.50  INTRA
1015 ILE   (  99-)  G      CG2 <-> 1016 GLU   ( 100-)  G      N      0.19    2.81  INTRA BF
 862 ILE   (  99-)  F      CG2 <->  863 GLU   ( 100-)  F      N      0.18    2.82  INTRA BL
 536 ARG   (  79-)  D      NH2 <->  558 ASP   ( 101-)  D      OD1    0.18    2.52  INTRA BL
 394 ASP   (  90-)  C      OD1 <->  396 ASP   (  92-)  C      N      0.18    2.52  INTRA BF
1006 ASP   (  90-)  G      OD1 <-> 1008 ASP   (  92-)  G      N      0.17    2.53  INTRA BF
1283 GLY   (  61-)  I      O   <-> 1365 ARG   ( 143-)  I      NH2    0.17    2.53  INTRA
1070 ALA   (   1-)  H      N   <-> 1222 GLN   ( 153-)  H      OE1    0.17    2.53  INTRA BF
1041 ASP   ( 125-)  G      O   <-> 1043 GLY   ( 127-)  G      N      0.17    2.53  INTRA BF
And so on for a total of 223 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.

1179 HIS   ( 110-)  H      -5.57
1092 LYS   (  23-)  H      -5.49
 432 LYS   ( 128-)  C      -5.45
1450 LYS   (  75-)  J      -5.41
 261 HIS   ( 110-)  B      -5.37
1044 LYS   ( 128-)  G      -5.31
1095 ASN   (  26-)  H      -5.29
 109 HIS   ( 110-)  A      -5.28
 480 LYS   (  23-)  D      -5.26
 720 HIS   ( 110-)  E      -5.26
 991 LYS   (  75-)  G      -5.25
1248 ASN   (  26-)  I      -5.23
 633 LYS   (  23-)  E      -5.22
 279 LYS   ( 128-)  B      -5.21
 585 LYS   ( 128-)  D      -5.21
1197 LYS   ( 128-)  H      -5.20
1350 LYS   ( 128-)  I      -5.18
 330 ASN   (  26-)  C      -5.15
 567 HIS   ( 110-)  D      -5.15
 738 LYS   ( 128-)  E      -5.15
1503 LYS   ( 128-)  J      -5.14
1144 LYS   (  75-)  H      -5.13
 483 ASN   (  26-)  D      -5.13
 685 LYS   (  75-)  E      -5.12
 127 LYS   ( 128-)  A      -5.10
1485 HIS   ( 110-)  J      -5.09
 891 LYS   ( 128-)  F      -5.08
  25 ASN   (  26-)  A      -5.05
 177 ASN   (  26-)  B      -5.00

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.

 983 LEU   (  67-)  G   -2.85

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.

1553 HOH   ( 661 )  E      O     50.97  134.42   46.38

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.

 109 HIS   ( 110-)  A

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.

  13 VAL   (  14-)  A      N
  51 ASP   (  52-)  A      N
  52 ASN   (  53-)  A      ND2
 130 ASN   ( 131-)  A      N
 135 LYS   ( 136-)  A      N
 203 ASP   (  52-)  B      N
 230 ARG   (  79-)  B      N
 356 ASP   (  52-)  C      N
 409 SER   ( 105-)  C      N
 409 SER   ( 105-)  C      OG
 417 ILE   ( 113-)  C      N
 438 SER   ( 134-)  C      OG
 483 ASN   (  26-)  D      N
 509 ASP   (  52-)  D      N
 662 ASP   (  52-)  E      N
 679 ARG   (  69-)  E      NE
 789 ASN   (  26-)  F      N
 815 ASP   (  52-)  F      N
 968 ASP   (  52-)  G      N
 981 ASN   (  65-)  G      N
 985 ARG   (  69-)  G      NE
 995 ARG   (  79-)  G      NH2
1026 HIS   ( 110-)  G      N
1029 ILE   ( 113-)  G      N
1072 LYS   (   3-)  H      N
1083 VAL   (  14-)  H      N
1121 ASP   (  52-)  H      N
1140 HIS   (  71-)  H      NE2
1157 THR   (  88-)  H      N
1178 ASP   ( 109-)  H      N
1179 HIS   ( 110-)  H      N
1275 ASN   (  53-)  I      ND2
1389 VAL   (  14-)  J      N
1427 ASP   (  52-)  J      N
1442 LEU   (  67-)  J      N
1485 HIS   ( 110-)  J      N
1506 ASN   ( 131-)  J      N
Only metal coordination for   62 HIS  (  63-) A      ND1
Only metal coordination for   70 HIS  (  71-) A      ND1
Only metal coordination for   79 HIS  (  80-) A      ND1
Only metal coordination for   82 ASP  (  83-) A      OD1
Only metal coordination for  214 HIS  (  63-) B      ND1
Only metal coordination for  222 HIS  (  71-) B      ND1
Only metal coordination for  231 HIS  (  80-) B      ND1
Only metal coordination for  234 ASP  (  83-) B      OD1
Only metal coordination for  367 HIS  (  63-) C      ND1
Only metal coordination for  375 HIS  (  71-) C      ND1
Only metal coordination for  384 HIS  (  80-) C      ND1
Only metal coordination for  387 ASP  (  83-) C      OD1
Only metal coordination for  520 HIS  (  63-) D      ND1
Only metal coordination for  528 HIS  (  71-) D      ND1
Only metal coordination for  537 HIS  (  80-) D      ND1
Only metal coordination for  540 ASP  (  83-) D      OD1
Only metal coordination for  673 HIS  (  63-) E      ND1
Only metal coordination for  681 HIS  (  71-) E      ND1
Only metal coordination for  690 HIS  (  80-) E      ND1
Only metal coordination for  693 ASP  (  83-) E      OD1
Only metal coordination for  826 HIS  (  63-) F      ND1
Only metal coordination for  834 HIS  (  71-) F      ND1
Only metal coordination for  843 HIS  (  80-) F      ND1
Only metal coordination for  846 ASP  (  83-) F      OD1
Only metal coordination for  979 HIS  (  63-) G      ND1
Only metal coordination for  987 HIS  (  71-) G      ND1
Only metal coordination for  996 HIS  (  80-) G      ND1
Only metal coordination for  999 ASP  (  83-) G      OD1
Only metal coordination for 1132 HIS  (  63-) H      ND1
Only metal coordination for 1140 HIS  (  71-) H      ND1
Only metal coordination for 1149 HIS  (  80-) H      ND1
Only metal coordination for 1152 ASP  (  83-) H      OD1
Only metal coordination for 1285 HIS  (  63-) I      ND1
Only metal coordination for 1293 HIS  (  71-) I      ND1
Only metal coordination for 1302 HIS  (  80-) I      ND1
Only metal coordination for 1305 ASP  (  83-) I      OD1
Only metal coordination for 1438 HIS  (  63-) J      ND1
Only metal coordination for 1446 HIS  (  71-) J      ND1
Only metal coordination for 1455 HIS  (  80-) J      ND1
Only metal coordination for 1458 ASP  (  83-) J      OD1

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.

  42 HIS   (  43-)  A      ND1
 109 HIS   ( 110-)  A      NE2

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.

1551 HOH   ( 609 )  C      O  0.95  K  4 Ion-B H2O-B
1554 HOH   ( 654 )  F      O  0.97  K  5 Ion-B

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.

  89 ASP   (  90-)  A   H-bonding suggests Asn
 124 ASP   ( 125-)  A   H-bonding suggests Asn
 241 ASP   (  90-)  B   H-bonding suggests Asn; but Alt-Rotamer
 413 ASP   ( 109-)  C   H-bonding suggests Asn; but Alt-Rotamer
 429 ASP   ( 125-)  C   H-bonding suggests Asn
 700 ASP   (  90-)  E   H-bonding suggests Asn; but Alt-Rotamer
 735 ASP   ( 125-)  E   H-bonding suggests Asn
 888 ASP   ( 125-)  F   H-bonding suggests Asn
1006 ASP   (  90-)  G   H-bonding suggests Asn; but Alt-Rotamer
1194 ASP   ( 125-)  H   H-bonding suggests Asn
1312 ASP   (  90-)  I   H-bonding suggests Asn; but Alt-Rotamer
1347 ASP   ( 125-)  I   H-bonding suggests Asn
1500 ASP   ( 125-)  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 :  -0.604
  2nd generation packing quality :   1.862
  Ramachandran plot appearance   :  -1.682
  chi-1/chi-2 rotamer normality  :  -0.992
  Backbone conformation          :  -0.010

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.374 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.294 (tight)
  Side chain planarity           :   0.289 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   1.405
  Inside/Outside distribution    :   0.941

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :   2.3
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :   0.6
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.374 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.294 (tight)
  Side chain planarity           :   0.289 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   1.405
  Inside/Outside distribution    :   0.941
==============

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.