WHAT IF Check report

This file was created 2011-12-17 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 pdb2rmc.ent

Checks that need to be done early-on in validation

Warning: Class of space group could be incorrect

The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file.

Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly.

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the space group: MONOCLINIC

Space group name: P 1 21 1

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 : 0.440
CA-only RMS fit for the two chains : 0.159

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 E

All-atom RMS fit for the two chains : 0.587
CA-only RMS fit for the two chains : 0.146

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 0.477
CA-only RMS fit for the two chains : 0.195

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and G

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 : 0.287
CA-only RMS fit for the two chains : 0.106

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.

 754 DAL   (   1-)  B  -
 755 MVA   (   4-)  B  -
 756 BMT   (   5-)  B  -
 757 ABA   (   6-)  B  -
 758 SAR   (   7-)  B  -
 760 DAL   (   1-)  D  -
 761 MVA   (   4-)  D  -
 762 BMT   (   5-)  D  -
 763 ABA   (   6-)  D  -
 764 SAR   (   7-)  D  -
 766 DAL   (   1-)  F  -
 767 MVA   (   4-)  F  -
 768 BMT   (   5-)  F  -
 769 ABA   (   6-)  F  -
 770 SAR   (   7-)  F  -
 772 SAR   (   7-)  H  -
 773 ABA   (   6-)  H  -
 774 BMT   (   5-)  H  -
 775 MVA   (   4-)  H  -
 776 DAL   (   1-)  H  -

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.

 183 MLE   (   2-)  B  -   N   bound to  754 DAL   (   1-)  B  -   C
 371 MLE   (   2-)  D  -   N   bound to  760 DAL   (   1-)  D  -   C
 559 MLE   (   2-)  F  -   N   bound to  766 DAL   (   1-)  F  -   C
 747 MLE   (   2-)  H  -   N   bound to  776 DAL   (   1-)  H  -   C

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: C

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: G

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 183 MLE   (   2-)  B
 184 MLE   (   3-)  B
 185 MLE   (   8-)  B
 187 MLE   (  10-)  B
 371 MLE   (   2-)  D
 372 MLE   (   3-)  D
 373 MLE   (   8-)  D
 375 MLE   (  10-)  D
 559 MLE   (   2-)  F
 560 MLE   (   3-)  F
 561 MLE   (   8-)  F
 563 MLE   (  10-)  F
 747 MLE   (   2-)  H
 748 MLE   (   3-)  H
 749 MLE   (   8-)  H
 751 MLE   (  10-)  H

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 LYS   (  31-)  A      CG
   1 LYS   (  31-)  A      CD
   1 LYS   (  31-)  A      CE
   1 LYS   (  31-)  A      NZ
   2 ARG   (  32-)  A      CG
   2 ARG   (  32-)  A      CD
   2 ARG   (  32-)  A      NE
   2 ARG   (  32-)  A      CZ
   2 ARG   (  32-)  A      NH1
   2 ARG   (  32-)  A      NH2
 189 LYS   (  31-)  C      CG
 189 LYS   (  31-)  C      CD
 189 LYS   (  31-)  C      CE
 189 LYS   (  31-)  C      NZ
 190 ARG   (  32-)  C      CG
 190 ARG   (  32-)  C      CD
 190 ARG   (  32-)  C      NE
 190 ARG   (  32-)  C      CZ
 190 ARG   (  32-)  C      NH1
 190 ARG   (  32-)  C      NH2
 377 LYS   (  31-)  E      CG
 377 LYS   (  31-)  E      CD
 377 LYS   (  31-)  E      CE
 377 LYS   (  31-)  E      NZ
 378 ARG   (  32-)  E      CG
 378 ARG   (  32-)  E      CD
 378 ARG   (  32-)  E      NE
 378 ARG   (  32-)  E      CZ
 378 ARG   (  32-)  E      NH1
 378 ARG   (  32-)  E      NH2
 565 LYS   (  31-)  G      CG
 565 LYS   (  31-)  G      CD
 565 LYS   (  31-)  G      CE
 565 LYS   (  31-)  G      NZ
 566 ARG   (  32-)  G      CG
 566 ARG   (  32-)  G      CD
 566 ARG   (  32-)  G      NE
 566 ARG   (  32-)  G      CZ
 566 ARG   (  32-)  G      NH1
 566 ARG   (  32-)  G      NH2

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:

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: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: G

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.

   8 ASP   (  38-)  A      CA   CB   CG  116.80    4.2
  11 PHE   (  41-)  A      CA   CB   CG  118.38    4.6
  12 PHE   (  42-)  A      CA   CB   CG  118.08    4.3
  57 PHE   (  87-)  A      CA   CB   CG  108.46   -5.3
  62 LYS   (  92-)  A      N    CA   CB  103.31   -4.2
  63 ASP   (  93-)  A      CA   CB   CG  117.67    5.1
  80 MET   ( 110-)  A      CA   CB   CG  104.29   -4.9
  85 GLU   ( 115-)  A      CA   CB   CG  102.38   -5.9
  87 PHE   ( 117-)  A      CA   CB   CG  119.39    5.6
  91 ASN   ( 121-)  A      CA   CB   CG  116.68    4.1
 101 TRP   ( 131-)  A      CB   CG   CD1 120.56   -4.2
 101 TRP   ( 131-)  A      CE3  CD2  CG  139.12    5.2
 101 TRP   ( 131-)  A      CG   CD2  CE2 101.34   -4.9
 117 PHE   ( 147-)  A      CA   CB   CG  118.56    4.8
 121 THR   ( 151-)  A      CA   CB   OG1 101.20   -5.6
 125 TRP   ( 155-)  A      CG   CD2  CE2 101.90   -4.4
 152 ASP   ( 182-)  A      CA   CB   CG  117.37    4.8
 157 PRO   ( 187-)  A     -CA  -C    N   123.25    4.2
 181 ASP   ( 211-)  A      CA   CB   CG  119.29    6.7
 182 TRP   ( 212-)  A      CD1  CG   CD2 112.97    4.2
 182 TRP   ( 212-)  A      CG   CD1  NE1 104.63   -4.3
 182 TRP   ( 212-)  A      CE3  CD2  CG  138.83    4.9
 182 TRP   ( 212-)  A      CG   CD2  CE2 101.17   -5.0
 196 ASP   (  38-)  C      CA   CB   CG  118.15    5.5
 197 LYS   (  39-)  C      CB   CG   CD  101.65   -4.2
And so on for a total of 94 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.

 565 LYS   (  31-)  G    5.36
 377 LYS   (  31-)  E    4.98
 553 VAL   ( 207-)  E    4.53
 284 HIS   ( 126-)  C    4.08

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.

 366 GLU   ( 208-)  C    5.47

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 318 HIS   ( 160-)  C      CB   6.17
 694 HIS   ( 160-)  G      CB   4.72
 130 HIS   ( 160-)  A      CB   4.68
 746 TRP   ( 212-)  G      CB   4.38
 473 TYR   ( 127-)  E      OH   4.18
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.097

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.

 180 PRO   ( 210-)  A    -3.1
 497 THR   ( 151-)  E    -3.0
 309 THR   ( 151-)  C    -3.0
 685 THR   ( 151-)  G    -3.0
 121 THR   ( 151-)  A    -3.0
 556 PRO   ( 210-)  E    -2.9
 499 PRO   ( 153-)  E    -2.7
 368 PRO   ( 210-)  C    -2.6
 123 PRO   ( 153-)  A    -2.4
 687 PRO   ( 153-)  G    -2.4
 311 PRO   ( 153-)  C    -2.4
 253 MET   (  95-)  C    -2.3
  65 MET   (  95-)  A    -2.3
 441 MET   (  95-)  E    -2.2
 629 MET   (  95-)  G    -2.2
 677 GLY   ( 143-)  G    -2.1
 301 GLY   ( 143-)  C    -2.1
 113 GLY   ( 143-)  A    -2.1
 489 GLY   ( 143-)  E    -2.1
 628 PHE   (  94-)  G    -2.1
  64 PHE   (  94-)  A    -2.1
 620 ILE   (  86-)  G    -2.0
  18 ASP   (  48-)  A    -2.0
 440 PHE   (  94-)  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.

  63 ASP   (  93-)  A  Poor phi/psi
  74 ARG   ( 104-)  A  Poor phi/psi
  75 ASP   ( 105-)  A  Poor phi/psi
 133 PHE   ( 163-)  A  Poor phi/psi
 155 ASP   ( 185-)  A  Poor phi/psi
 180 PRO   ( 210-)  A  Poor phi/psi
 251 ASP   (  93-)  C  Poor phi/psi
 253 MET   (  95-)  C  Poor phi/psi
 262 ARG   ( 104-)  C  Poor phi/psi
 279 ASN   ( 121-)  C  Poor phi/psi
 321 PHE   ( 163-)  C  Poor phi/psi
 343 ASP   ( 185-)  C  Poor phi/psi
 439 ASP   (  93-)  E  Poor phi/psi
 450 ARG   ( 104-)  E  Poor phi/psi
 451 ASP   ( 105-)  E  Poor phi/psi
 467 ASN   ( 121-)  E  Poor phi/psi
 509 PHE   ( 163-)  E  Poor phi/psi
 531 ASP   ( 185-)  E  Poor phi/psi
 556 PRO   ( 210-)  E  Poor phi/psi
 627 ASP   (  93-)  G  Poor phi/psi
 655 ASN   ( 121-)  G  Poor phi/psi
 674 ASP   ( 140-)  G  Poor phi/psi
 678 SER   ( 144-)  G  Poor phi/psi
 697 PHE   ( 163-)  G  Poor phi/psi
 719 ASP   ( 185-)  G  Poor phi/psi
 745 ASP   ( 211-)  G  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.825

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.

 335 GLU   ( 177-)  C    0.33
 333 SER   ( 175-)  C    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!

   7 THR   (  37-)  A      0
   8 ASP   (  38-)  A      0
  18 ASP   (  48-)  A      0
  21 VAL   (  51-)  A      0
  29 PHE   (  59-)  A      0
  33 VAL   (  63-)  A      0
  47 GLU   (  77-)  A      0
  48 LYS   (  78-)  A      0
  50 TYR   (  80-)  A      0
  52 TYR   (  82-)  A      0
  53 LYS   (  83-)  A      0
  55 SER   (  85-)  A      0
  57 PHE   (  87-)  A      0
  58 HIS   (  88-)  A      0
  62 LYS   (  92-)  A      0
  64 PHE   (  94-)  A      0
  65 MET   (  95-)  A      0
  71 PHE   ( 101-)  A      0
  72 THR   ( 102-)  A      0
  73 ALA   ( 103-)  A      0
  74 ARG   ( 104-)  A      0
  75 ASP   ( 105-)  A      0
  77 THR   ( 107-)  A      0
  83 TYR   ( 113-)  A      0
  85 GLU   ( 115-)  A      0
And so on for a total of 371 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!

 581 GLY   (  47-)  G   2.17   10

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].

 123 PRO   ( 153-)  A   -64.8 envelop C-beta (-72 degrees)
 157 PRO   ( 187-)  A  -118.1 half-chair C-delta/C-gamma (-126 degrees)
 180 PRO   ( 210-)  A  -153.3 half-chair N/C-delta (-162 degrees)
 368 PRO   ( 210-)  C  -124.9 half-chair C-delta/C-gamma (-126 degrees)
 556 PRO   ( 210-)  E  -124.7 half-chair C-delta/C-gamma (-126 degrees)
 721 PRO   ( 187-)  G  -121.5 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 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.

 752 ALA   (  11-)  H      C   <->  776 DAL   (   1-)  H      N      1.37    1.33  INTRA B3
 773 ABA   (   6-)  H      N   <->  774 BMT   (   5-)  H      C      1.37    1.33  INTRA BL
 749 MLE   (   8-)  H      N   <->  772 SAR   (   7-)  H      C      1.36    1.34  INTRA B3
 772 SAR   (   7-)  H      N   <->  773 ABA   (   6-)  H      C      1.36    1.34  INTRA BL
 747 MLE   (   2-)  H      N   <->  776 DAL   (   1-)  H      C      1.36    1.34  INTRA B3
 748 MLE   (   3-)  H      C   <->  775 MVA   (   4-)  H      N      1.36    1.34  INTRA BL
 774 BMT   (   5-)  H      N   <->  775 MVA   (   4-)  H      C      1.34    1.36  INTRA BL
 749 MLE   (   8-)  H      CA  <->  772 SAR   (   7-)  H      C      0.81    2.39  INTRA
 774 BMT   (   5-)  H      CA  <->  775 MVA   (   4-)  H      C      0.79    2.41  INTRA BL
 747 MLE   (   2-)  H      CA  <->  776 DAL   (   1-)  H      C      0.77    2.43  INTRA BL
 747 MLE   (   2-)  H      CN  <->  776 DAL   (   1-)  H      C      0.74    2.46  INTRA
 749 MLE   (   8-)  H      CN  <->  772 SAR   (   7-)  H      C      0.74    2.46  INTRA
 752 ALA   (  11-)  H      CA  <->  776 DAL   (   1-)  H      N      0.70    2.40  INTRA
 774 BMT   (   5-)  H      CN  <->  775 MVA   (   4-)  H      C      0.69    2.51  INTRA BL
 773 ABA   (   6-)  H      CA  <->  774 BMT   (   5-)  H      C      0.67    2.43  INTRA BL
 748 MLE   (   3-)  H      CA  <->  775 MVA   (   4-)  H      N      0.59    2.51  INTRA BL
 772 SAR   (   7-)  H      CN  <->  773 ABA   (   6-)  H      C      0.58    2.52  INTRA BL
 772 SAR   (   7-)  H      CA  <->  773 ABA   (   6-)  H      C      0.56    2.44  INTRA BL
 748 MLE   (   3-)  H      O   <->  775 MVA   (   4-)  H      N      0.47    2.23  INTRA BL
 752 ALA   (  11-)  H      O   <->  776 DAL   (   1-)  H      N      0.43    2.27  INTRA
 774 BMT   (   5-)  H      CN  <->  775 MVA   (   4-)  H      CA     0.33    2.87  INTRA BL
 122 LYS   ( 152-)  A      NZ  <->  777 HOH   (2065 )  A      O      0.31    2.39  INTRA
 747 MLE   (   2-)  H      CN  <->  776 DAL   (   1-)  H      CA     0.28    2.92  INTRA
 749 MLE   (   8-)  H      CN  <->  772 SAR   (   7-)  H      CA     0.27    2.93  INTRA
 223 LYS   (  65-)  C      NZ  <->  778 HOH   (2020 )  C      O      0.26    2.44  INTRA BF
And so on for a total of 110 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

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.

 360 LYS   ( 202-)  C      -6.11
 172 LYS   ( 202-)  A      -6.10
 736 LYS   ( 202-)  G      -6.07
 548 LYS   ( 202-)  E      -6.04
 238 TYR   (  80-)  C      -5.67
 366 GLU   ( 208-)  C      -5.55
  74 ARG   ( 104-)  A      -5.55
 450 ARG   ( 104-)  E      -5.48
 285 TYR   ( 127-)  C      -5.46
 473 TYR   ( 127-)  E      -5.44
  97 TYR   ( 127-)  A      -5.43
 638 ARG   ( 104-)  G      -5.41
 742 GLU   ( 208-)  G      -5.39
 426 TYR   (  80-)  E      -5.37
 562 VAL   (   9-)  F      -5.36
 178 GLU   ( 208-)  A      -5.33
 750 VAL   (   9-)  H      -5.32
 374 VAL   (   9-)  D      -5.28
 554 GLU   ( 208-)  E      -5.28
 262 ARG   ( 104-)  C      -5.27
 661 TYR   ( 127-)  G      -5.26
 186 VAL   (   9-)  B      -5.25

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: 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: 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: G

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.

 566 ARG   (  32-)  G   -2.88
 378 ARG   (  32-)  E   -2.75

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: C

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: G

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.

 337 GLN   ( 179-)  C
 525 GLN   ( 179-)  E
 708 HIS   ( 174-)  G
 713 GLN   ( 179-)  G

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.

  50 TYR   (  80-)  A      N
  91 ASN   ( 121-)  A      N
  98 GLY   ( 128-)  A      N
 106 ASN   ( 136-)  A      N
 121 THR   ( 151-)  A      N
 159 THR   ( 189-)  A      N
 203 ARG   (  45-)  C      NE
 274 THR   ( 116-)  C      N
 279 ASN   ( 121-)  C      N
 286 GLY   ( 128-)  C      N
 294 ASN   ( 136-)  C      N
 309 THR   ( 151-)  C      N
 467 ASN   ( 121-)  E      N
 474 GLY   ( 128-)  E      N
 482 ASN   ( 136-)  E      N
 497 THR   ( 151-)  E      N
 530 HIS   ( 184-)  E      N
 614 TYR   (  80-)  G      N
 655 ASN   ( 121-)  G      N
 659 LYS   ( 125-)  G      N
 661 TYR   ( 127-)  G      OH
 670 ASN   ( 136-)  G      N
 685 THR   ( 151-)  G      N

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 777 HOH   (2070 )  A      O  0.89  K  4
 778 HOH   (2083 )  C      O  1.01  K  4
 779 HOH   (2030 )  E      O  1.12  K  4

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.

 528 ASP   ( 182-)  E   H-bonding suggests Asn; but Alt-Rotamer
 554 GLU   ( 208-)  E   H-bonding suggests Gln
 742 GLU   ( 208-)  G   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.978
  2nd generation packing quality :  -1.194
  Ramachandran plot appearance   :  -1.097
  chi-1/chi-2 rotamer normality  :  -0.825
  Backbone conformation          :  -0.431

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.704
  Bond angles                    :   1.321
  Omega angle restraints         :   0.796
  Side chain planarity           :   1.159
  Improper dihedral distribution :   1.167
  B-factor distribution          :   0.765
  Inside/Outside distribution    :   0.950

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 : 1.64


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.704
  Bond angles                    :   1.321
  Omega angle restraints         :   0.796
  Side chain planarity           :   1.159
  Improper dihedral distribution :   1.167
  B-factor distribution          :   0.765
  Inside/Outside distribution    :   0.950
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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Symmetry Checks
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Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
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      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.