WHAT IF Check report

This file was created 2011-12-16 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 pdb3iai.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 : 0.579
CA-only RMS fit for the two chains : 0.252

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 : 0.588
CA-only RMS fit for the two chains : 0.278

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 : 0.761
CA-only RMS fit for the two chains : 0.572

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 : 0.286
CA-only RMS fit for the two chains : 0.098

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.339
CA-only RMS fit for the two chains : 0.138

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: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 114801.977
Volume of the Unit Cell V= 3760531.3
Space group multiplicity: 6
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.459
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 5.560

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.

1028 AZM   ( 263-)  A  -
1029 BMA   ( 266-)  A  -
1030 MAN   ( 267-)  A  -
1031 MAN   ( 268-)  A  -
1038 TRS   ( 501-)  A  -
1042 AZM   ( 263-)  B  -
1044 BMA   ( 266-)  B  -
1045 MAN   ( 267-)  B  -
1046 MAN   ( 268-)  B  -
1052 TRS   ( 501-)  B  -
1055 AZM   ( 263-)  C  -
1057 BMA   ( 266-)  C  -
1058 MAN   ( 267-)  C  -
1059 MAN   ( 268-)  C  -
1064 TRS   ( 501-)  C  -
1068 MAN   ( 267-)  D  -
1077 TRS   ( 501-)  D  -
1078 MAN   ( 268-)  D  -
1079 BMA   ( 266-)  D  -
1080 AZM   ( 263-)  D  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

1015 NAG   ( 264-)  A  -   O4  bound to 1016 NAG   ( 265-)  A  -   C1
1016 NAG   ( 265-)  A  -   O4  bound to 1029 BMA   ( 266-)  A  -   C1
1017 NAG   ( 264-)  B  -   O4  bound to 1018 NAG   ( 265-)  B  -   C1
1018 NAG   ( 265-)  B  -   O4  bound to 1044 BMA   ( 266-)  B  -   C1
1019 NAG   ( 264-)  C  -   O4  bound to 1020 NAG   ( 265-)  C  -   C1
1020 NAG   ( 265-)  C  -   O4  bound to 1057 BMA   ( 266-)  C  -   C1
1021 NAG   ( 264-)  D  -   O4  bound to 1022 NAG   ( 265-)  D  -   C1
1022 NAG   ( 265-)  D  -   O4  bound to 1079 BMA   ( 266-)  D  -   C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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

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

   9 TYR   (   7-)  A
 193 TYR   ( 194-)  A
 261 TYR   (   7-)  B
 445 TYR   ( 194-)  B
 513 TYR   (   7-)  C
 697 TYR   ( 194-)  C
 766 TYR   (   7-)  D
 950 TYR   ( 194-)  D

Warning: Phenylalanine convention problem

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

  26 PHE   (  27-)  A
  39 PHE   (  40-)  A
 144 PHE   ( 147-)  A
 187 PHE   ( 189-)  A
 191 PHE   ( 192-)  A
 211 PHE   ( 212-)  A
 278 PHE   (  27-)  B
 291 PHE   (  40-)  B
 396 PHE   ( 147-)  B
 439 PHE   ( 189-)  B
 443 PHE   ( 192-)  B
 463 PHE   ( 212-)  B
 530 PHE   (  27-)  C
 543 PHE   (  40-)  C
 648 PHE   ( 147-)  C
 691 PHE   ( 189-)  C
 695 PHE   ( 192-)  C
 715 PHE   ( 212-)  C
 783 PHE   (  27-)  D
 796 PHE   (  40-)  D
 901 PHE   ( 147-)  D
 944 PHE   ( 189-)  D
 948 PHE   ( 192-)  D
 968 PHE   ( 212-)  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.

  31 ASP   (  32-)  A
 283 ASP   (  32-)  B
 535 ASP   (  32-)  C
 788 ASP   (  32-)  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.

  47 GLU   (  48-)  A
  77 GLU   (  78-)  A
 164 GLU   ( 166-)  A
 167 GLU   ( 169-)  A
 253 GLU   ( 257-)  A
 299 GLU   (  48-)  B
 329 GLU   (  78-)  B
 416 GLU   ( 166-)  B
 505 GLU   ( 257-)  B
 551 GLU   (  48-)  C
 581 GLU   (  78-)  C
 655 GLU   ( 153-)  C
 668 GLU   ( 166-)  C
 757 GLU   ( 257-)  C
 804 GLU   (  48-)  D
 834 GLU   (  78-)  D
1010 GLU   ( 257-)  D

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998843  0.000019  0.000104|
 |  0.000019  0.999197  0.000038|
 |  0.000104  0.000038  0.998684|
Proposed new scale matrix

 |  0.006944  0.004007  0.000000|
 |  0.000000  0.008015  0.000000|
 |  0.000000  0.000000  0.004793|
With corresponding cell

    A    = 144.011  B   = 144.043  C    = 208.624
    Alpha=  90.001  Beta=  90.002  Gamma= 119.988

The CRYST1 cell dimensions

    A    = 144.180  B   = 144.180  C    = 208.890
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 42.626
(Under-)estimated Z-score: 4.812

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.

  68 VAL   (  66-)  A      N    CA   C   100.00   -4.0
 212 ASN   ( 213-)  A      CB   CG   ND2 123.47    4.7
 464 ASN   ( 213-)  B      CB   CG   ND2 123.39    4.7
 716 ASN   ( 213-)  C      CB   CG   ND2 123.31    4.6
 969 ASN   ( 213-)  D      CB   CG   ND2 123.62    4.8

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.

  31 ASP   (  32-)  A
  47 GLU   (  48-)  A
  77 GLU   (  78-)  A
 164 GLU   ( 166-)  A
 167 GLU   ( 169-)  A
 253 GLU   ( 257-)  A
 283 ASP   (  32-)  B
 299 GLU   (  48-)  B
 329 GLU   (  78-)  B
 416 GLU   ( 166-)  B
 505 GLU   ( 257-)  B
 535 ASP   (  32-)  C
 551 GLU   (  48-)  C
 581 GLU   (  78-)  C
 655 GLU   ( 153-)  C
 668 GLU   ( 166-)  C
 757 GLU   ( 257-)  C
 788 ASP   (  32-)  D
 804 GLU   (  48-)  D
 834 GLU   (  78-)  D
1010 GLU   ( 257-)  D

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.

 197 LEU   ( 198-)  A    4.02

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.

 177 LEU   ( 179-)  A    -2.5
  87 ARG   (  89-)  A    -2.4
 946 ARG   ( 190-)  D    -2.4
 681 LEU   ( 179-)  C    -2.4
 429 LEU   ( 179-)  B    -2.3
 848 LEU   (  93-)  D    -2.3
 360 GLU   ( 110-)  B    -2.2
 343 LEU   (  93-)  B    -2.2
 934 LEU   ( 179-)  D    -2.2
 615 ARG   ( 113-)  C    -2.2
 595 LEU   (  93-)  C    -2.2
 865 GLU   ( 110-)  D    -2.2
  91 LEU   (  93-)  A    -2.2
 342 GLN   (  92-)  B    -2.2
 847 GLN   (  92-)  D    -2.2
  90 GLN   (  92-)  A    -2.2
 594 GLN   (  92-)  C    -2.1
 612 GLU   ( 110-)  C    -2.1
 424 THR   ( 174-)  B    -2.1
 693 ARG   ( 190-)  C    -2.1
  29 PRO   (  30-)  A    -2.1
 676 THR   ( 174-)  C    -2.1
 108 GLU   ( 110-)  A    -2.1
 929 THR   ( 174-)  D    -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.

  12 ASP   (  10-)  A  PRO omega poor
  28 SER   (  29-)  A  PRO omega poor
  56 LEU   (  54-)  A  PRO omega poor
  67 SER   (  65-)  A  Poor phi/psi
 108 GLU   ( 110-)  A  Poor phi/psi
 200 PRO   ( 201-)  A  PRO omega poor
 202 CYS   ( 203-)  A  Poor phi/psi
 264 ASP   (  10-)  B  PRO omega poor
 280 SER   (  29-)  B  PRO omega poor
 308 LEU   (  54-)  B  PRO omega poor
 319 SER   (  65-)  B  Poor phi/psi
 360 GLU   ( 110-)  B  Poor phi/psi
 452 PRO   ( 201-)  B  PRO omega poor
 516 ASP   (  10-)  C  PRO omega poor
 532 SER   (  29-)  C  PRO omega poor
 560 LEU   (  54-)  C  PRO omega poor
 571 SER   (  65-)  C  Poor phi/psi
 612 GLU   ( 110-)  C  Poor phi/psi
 704 PRO   ( 201-)  C  PRO omega poor
 769 ASP   (  10-)  D  PRO omega poor
 785 SER   (  29-)  D  PRO omega poor
 813 LEU   (  54-)  D  PRO omega poor
 824 SER   (  65-)  D  Poor phi/psi
 865 GLU   ( 110-)  D  Poor phi/psi
 957 PRO   ( 201-)  D  PRO omega poor
 chi-1/chi-2 correlation Z-score : -0.737

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.

 415 GLU   ( 165-)  B    0.36
 667 GLU   ( 165-)  C    0.36
 917 SER   ( 162-)  D    0.36
 920 GLU   ( 165-)  D    0.36

Warning: Unusual backbone conformations

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

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

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

   6 HIS   (   4-)  A      0
   7 TRP   (   5-)  A      0
   9 TYR   (   7-)  A      0
  12 ASP   (  10-)  A      0
  13 PRO   (  11-)  A      0
  14 PRO   (  15-)  A      0
  18 VAL   (  19-)  A      0
  26 PHE   (  27-)  A      0
  27 GLN   (  28-)  A      0
  28 SER   (  29-)  A      0
  39 PHE   (  40-)  A      0
  49 LEU   (  50-)  A      0
  51 PHE   (  51-)  A      0
  52 GLN   (  52-)  A      0
  55 PRO   (  54-)  A      0
  56 LEU   (  54-)  A      0
  58 GLU   (  56-)  A      0
  62 ARG   (  60-)  A      0
  64 ASN   (  62-)  A      0
  66 HIS   (  64-)  A      0
  74 PRO   (  72-)  A      0
  80 LEU   (  81-)  A      0
  82 PRO   (  84-)  A      0
  85 GLU   (  87-)  A      0
  90 GLN   (  92-)  A      0
And so on for a total of 463 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 : 1.277

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!

  96 GLY   (  98-)  A   2.38   10

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.

1022 NAG   ( 265-)  D      O4  <-> 1079 BMA   ( 266-)  D      C1     1.01    1.39  INTRA B3
1022 NAG   ( 265-)  D      C4  <-> 1079 BMA   ( 266-)  D      C1     0.79    2.41  INTRA
  52 GLN   (  52-)  A      NE2 <-> 1081 HOH   (1574 )  A      O      0.34    2.36  INTRA BF
 615 ARG   ( 113-)  C      NH1 <-> 1083 HOH   (1018 )  C      O      0.32    2.38  INTRA
 817 ARG   (  58-)  D      NH2 <->  928 GLU   ( 173-)  D      OE1    0.29    2.41  INTRA
 792 GLN   (  36-)  D      NE2 <-> 1084 HOH   (1483 )  D      O      0.29    2.41  INTRA BF
 287 GLN   (  36-)  B      NE2 <-> 1082 HOH   (1191 )  B      O      0.28    2.42  INTRA BF
 604 ARG   ( 102-)  C      NH2 <-> 1083 HOH   (1607 )  C      O      0.25    2.45  INTRA BF
 304 GLN   (  52-)  B      NE2 <-> 1082 HOH   ( 541 )  B      O      0.24    2.46  INTRA
 841 ARG   (  86-)  D      NH1 <-> 1084 HOH   ( 329 )  D      O      0.23    2.47  INTRA
  33 ARG   (  34-)  A      NH1 <->   35 GLN   (  36-)  A      CD     0.23    2.87  INTRA BF
 591 ARG   (  89-)  C      NH2 <->  629 PHE   ( 128-)  C      O      0.22    2.48  INTRA
 539 GLN   (  36-)  C      NE2 <-> 1083 HOH   (1329 )  C      O      0.21    2.49  INTRA BF
 857 ARG   ( 102-)  D      NH2 <-> 1084 HOH   (1003 )  D      O      0.20    2.50  INTRA
 204 GLN   ( 205-)  A      NE2 <-> 1081 HOH   (1287 )  A      O      0.19    2.51  INTRA
 819 ARG   (  60-)  D      NH1 <-> 1084 HOH   (1437 )  D      O      0.19    2.51  INTRA BF
 537 ARG   (  34-)  C      NH1 <-> 1083 HOH   (1207 )  C      O      0.18    2.52  INTRA BF
 437 SER   ( 187-)  B    A OG  <->  465 GLN   ( 214-)  B      NE2    0.18    2.52  INTRA
 884 ARG   ( 130-)  D      NH2 <-> 1084 HOH   (1237 )  D      O      0.18    2.52  INTRA BF
 619 GLU   ( 117-)  C      OE2 <->  621 HIS   ( 119-)  C      NE2    0.17    2.53  INTRA BL
  62 ARG   (  60-)  A      NE  <-> 1081 HOH   ( 535 )  A      O      0.16    2.54  INTRA
 690 ASP   ( 188-)  C      N   <->  717 GLN   ( 214-)  C      NE2    0.16    2.69  INTRA
 367 GLU   ( 117-)  B      OE2 <->  369 HIS   ( 119-)  B      NE2    0.15    2.55  INTRA BL
 801 ARG   (  45-)  D      NE  <-> 1084 HOH   ( 310 )  D      O      0.15    2.55  INTRA
 456 GLN   ( 205-)  B      NE2 <-> 1082 HOH   ( 603 )  B      O      0.14    2.56  INTRA
And so on for a total of 107 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.

  56 LEU   (  54-)  A      -6.93
 813 LEU   (  54-)  D      -6.90
 560 LEU   (  54-)  C      -6.89
 308 LEU   (  54-)  B      -6.85
   8 ARG   (   6-)  A      -6.62
 260 ARG   (   6-)  B      -6.41
 512 ARG   (   6-)  C      -6.40
 100 ARG   ( 102-)  A      -6.39
 857 ARG   ( 102-)  D      -6.31
 604 ARG   ( 102-)  C      -6.26
 352 ARG   ( 102-)  B      -6.25
 765 ARG   (   6-)  D      -6.20
 363 ARG   ( 113-)  B      -6.04
 868 ARG   ( 113-)  D      -5.91
 556 GLN   (  52-)  C      -5.91
 111 ARG   ( 113-)  A      -5.88
 304 GLN   (  52-)  B      -5.81
 615 ARG   ( 113-)  C      -5.78
  52 GLN   (  52-)  A      -5.23
 809 GLN   (  52-)  D      -5.14
 296 ARG   (  45-)  B      -5.10
  44 ARG   (  45-)  A      -5.07

Warning: Abnormal packing environment for sequential residues

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

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

   8 ARG   (   6-)  A        10 - GLY      8- ( A)         -5.26
 260 ARG   (   6-)  B       262 - GLY      8- ( B)         -5.10
 512 ARG   (   6-)  C       514 - GLY      8- ( C)         -5.07
 765 ARG   (   6-)  D       767 - GLY      8- ( D)         -4.94

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.

  64 ASN   (  62-)  A   -2.88
 601 ALA   (  99-)  C   -2.84
 349 ALA   (  99-)  B   -2.84
 854 ALA   (  99-)  D   -2.82
  97 ALA   (  99-)  A   -2.82
 495 ALA   ( 247-)  B   -2.66
 243 ALA   ( 247-)  A   -2.65
 747 ALA   ( 247-)  C   -2.64
 275 ALA   (  24-)  B   -2.64
 780 ALA   (  24-)  D   -2.63
 539 GLN   (  36-)  C   -2.62
 181 ALA   ( 183-)  A   -2.61
1000 ALA   ( 247-)  D   -2.60
 792 GLN   (  36-)  D   -2.59
 685 ALA   ( 183-)  C   -2.58
 433 ALA   ( 183-)  B   -2.56

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

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.

1081 HOH   ( 823 )  A      O      8.35   72.10  -10.56
1081 HOH   ( 954 )  A      O     38.09   84.02  -22.84
1081 HOH   (1068 )  A      O      9.92   73.91  -21.78
1081 HOH   (1119 )  A      O     73.79   46.62  -50.91
1081 HOH   (1428 )  A      O     61.85   41.56  -51.12
1081 HOH   (1576 )  A      O     12.94   82.95   -4.23
1081 HOH   (1634 )  A      O     63.52   40.28  -52.64
1082 HOH   ( 751 )  B      O     45.21   63.75  -38.42
1082 HOH   ( 874 )  B      O     47.53   64.88  -37.84
1082 HOH   ( 955 )  B      O     43.96   50.18  -32.88
1082 HOH   (1179 )  B      O     44.09   49.51  -48.42
1082 HOH   (1180 )  B      O     44.24   47.56  -46.20
1082 HOH   (1181 )  B      O     41.79   47.05  -45.02
1082 HOH   (1187 )  B      O     49.99   79.18  -34.55
1082 HOH   (1480 )  B      O     36.70   61.60  -26.54
1083 HOH   ( 419 )  C      O    105.13   66.89    3.61
1083 HOH   ( 806 )  C      O     87.04   72.38   11.77
1083 HOH   ( 986 )  C      O     83.87   54.49   14.65
1083 HOH   (1564 )  C      O     78.81   50.44   34.08
1084 HOH   ( 597 )  D      O     67.64   48.09   34.75

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1082 HOH   (1497 )  B      O
Bound group on Asn; dont flip  212 ASN  ( 213-) A
Bound to: 1015 NAG  ( 264-) A
Bound group on Asn; dont flip  464 ASN  ( 213-) B
Bound to: 1017 NAG  ( 264-) B
Bound group on Asn; dont flip  716 ASN  ( 213-) C
Bound to: 1019 NAG  ( 264-) C
Bound group on Asn; dont flip  969 ASN  ( 213-) D
Bound to: 1021 NAG  ( 264-) D
Metal-coordinating Histidine residue  92 fixed to   1
Metal-coordinating Histidine residue  94 fixed to   1
Metal-coordinating Histidine residue 117 fixed to   1
Metal-coordinating Histidine residue 344 fixed to   1
Metal-coordinating Histidine residue 346 fixed to   1
Metal-coordinating Histidine residue 369 fixed to   1
Metal-coordinating Histidine residue 596 fixed to   1
Metal-coordinating Histidine residue 598 fixed to   1
Metal-coordinating Histidine residue 621 fixed to   1
Metal-coordinating Histidine residue 849 fixed to   1
Metal-coordinating Histidine residue 851 fixed to   1
Metal-coordinating Histidine residue 874 fixed to   1

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.

 213 GLN   ( 214-)  A
 425 GLN   ( 175-)  B
 717 GLN   ( 214-)  C
 727 HIS   ( 224-)  C
 930 GLN   ( 175-)  D
 970 GLN   ( 214-)  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.

   7 TRP   (   5-)  A      N
   9 TYR   (   7-)  A      OH
  30 VAL   (  31-)  A      N
  81 GLY   (  82-)  A      N
 111 ARG   ( 113-)  A      NH2
 177 LEU   ( 179-)  A      N
 189 ARG   ( 190-)  A      N
 199 THR   ( 200-)  A      N
 203 ALA   ( 204-)  A      N
 243 ALA   ( 247-)  A      N
 256 PHE   ( 260-)  A      N
 280 SER   (  29-)  B      OG
 282 VAL   (  31-)  B      N
 312 ARG   (  58-)  B      NE
 333 GLY   (  82-)  B      N
 363 ARG   ( 113-)  B      NH2
 429 LEU   ( 179-)  B      N
 445 TYR   ( 194-)  B      OH
 451 THR   ( 200-)  B      N
 455 ALA   ( 204-)  B      N
 487 SER   ( 239-)  B      N
 488 ARG   ( 240-)  B      NE
 495 ALA   ( 247-)  B      N
 508 PHE   ( 260-)  B      N
 534 VAL   (  31-)  C      N
And so on for a total of 56 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.

   3 ASP   (   0-)  A      OD1
  77 GLU   (  78-)  A      OE1
 120 HIS   ( 122-)  A      NE2
 329 GLU   (  78-)  B      OE1
 372 HIS   ( 122-)  B      NE2
 581 GLU   (  78-)  C      OE1
 624 HIS   ( 122-)  C      NE2
 834 GLU   (  78-)  D      OE1
 877 HIS   ( 122-)  D      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.

1081 HOH   ( 236 )  A      O  0.91  K  6
1081 HOH   ( 272 )  A      O  1.02  K  4
1081 HOH   ( 340 )  A      O  1.05  K  5
1081 HOH   (1576 )  A      O  1.12  K  5 Ion-B
1082 HOH   ( 332 )  B      O  1.12  K  4
1082 HOH   ( 778 )  B      O  0.87  K  4 Ion-B
1082 HOH   ( 980 )  B      O  1.13  K  4 Ion-B
1083 HOH   ( 277 )  C      O  1.05  K  4
1083 HOH   ( 572 )  C      O  1.11  K  5
1083 HOH   (1624 )  C      O  1.07  K  5 ION-B
1084 HOH   ( 311 )  D      O  1.01  K  4
1084 HOH   ( 356 )  D      O  1.04  K  4
1084 HOH   ( 705 )  D      O  1.00  K  4
1084 HOH   ( 771 )  D      O  1.08  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.

  77 GLU   (  78-)  A   H-bonding suggests Gln; but Alt-Rotamer
 147 GLU   ( 150-)  A   H-bonding suggests Gln
 168 GLU   ( 170-)  A   H-bonding suggests Gln; Ligand-contact
 399 GLU   ( 150-)  B   H-bonding suggests Gln
 651 GLU   ( 150-)  C   H-bonding suggests Gln
 834 GLU   (  78-)  D   H-bonding suggests Gln; but Alt-Rotamer
 904 GLU   ( 150-)  D   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 :  -0.449
  2nd generation packing quality :  -1.922
  Ramachandran plot appearance   :  -1.148
  chi-1/chi-2 rotamer normality  :  -0.737
  Backbone conformation          :  -1.098

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.265 (tight)
  Bond angles                    :   0.633 (tight)
  Omega angle restraints         :   0.232 (tight)
  Side chain planarity           :   0.239 (tight)
  Improper dihedral distribution :   0.533
  B-factor distribution          :   0.547
  Inside/Outside distribution    :   0.967

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.265 (tight)
  Bond angles                    :   0.633 (tight)
  Omega angle restraints         :   0.232 (tight)
  Side chain planarity           :   0.239 (tight)
  Improper dihedral distribution :   0.533
  B-factor distribution          :   0.547
  Inside/Outside distribution    :   0.967
==============

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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      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
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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,
      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?
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Checking checks
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      Who checks the checkers
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