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 pdb1pth.ent

Checks that need to be done early-on in validation

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: 127487.594
Volume of the Unit Cell V= 4910016.5
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
but the number of MTRIX matrices flagged as `do not use` = 1
which seems more or less consistent with the SEQRES multiplicity
because the unitary MTRIX record gets forgotten more often ...
Matthews coefficient for observed atoms and Z high: Vm= 4.814
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.630

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.

1111 BOG   ( 702-)  A  -
1112 SAL   ( 710-)  A  -
1115 SAL   ( 711-)  B  -
1116 BOG   ( 702-)  B  -

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.

1104 NAG   ( 671-)  A  -   O4  bound to 1105 NAG   ( 672-)  A  -   C1
1108 NAG   ( 671-)  B  -   O4  bound to 1109 NAG   ( 672-)  B  -   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

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.

 498 0AH   ( 530-)  A
1049 0AH   ( 530-)  B

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.

  41 GLU   (  73-)  A    High
  43 TRP   (  75-)  A    High
  47 ARG   (  79-)  A    High
  51 ARG   (  83-)  A    High
  65 ARG   (  97-)  A    High
 125 ARG   ( 157-)  A    High
 138 GLN   ( 170-)  A    High
 154 LYS   ( 186-)  A    High
 207 GLU   ( 239-)  A    High
 235 GLU   ( 267-)  A    High
 236 GLU   ( 268-)  A    High
 245 ARG   ( 277-)  A    High
 364 ARG   ( 396-)  A    High
 461 GLU   ( 493-)  A    High
 521 GLU   ( 553-)  A    High
 592 GLU   (  73-)  B    High
 594 TRP   (  75-)  B    High
 598 ARG   (  79-)  B    High
 602 ARG   (  83-)  B    High
 616 ARG   (  97-)  B    High
 676 ARG   ( 157-)  B    High
 689 GLN   ( 170-)  B    High
 705 LYS   ( 186-)  B    High
 758 GLU   ( 239-)  B    High
 786 GLU   ( 267-)  B    High
 787 GLU   ( 268-)  B    High
 796 ARG   ( 277-)  B    High
 915 ARG   ( 396-)  B    High
1012 GLU   ( 493-)  B    High
1072 GLU   ( 553-)  B    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:

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.

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 16.79

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

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

 |  1.002085  0.000340  0.000216|
 |  0.000340  1.001690  0.000445|
 |  0.000216  0.000445  1.001444|
Proposed new scale matrix

 |  0.010022 -0.000003 -0.000002|
 | -0.000002  0.004758 -0.000002|
 |  0.000000 -0.000002  0.004249|
With corresponding cell

    A    =  99.779  B   = 210.174  C    = 235.357
    Alpha=  89.949  Beta=  89.989  Gamma=  89.961

The CRYST1 cell dimensions

    A    =  99.570  B   = 209.800  C    = 235.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 121.607
(Under-)estimated Z-score: 8.127

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.

 116 TYR   ( 148-)  A      N    CA   C    98.10   -4.7
 123 VAL   ( 155-)  A      N    CA   C    99.84   -4.1
 172 HIS   ( 204-)  A      CG   ND1  CE1 109.70    4.1
 178 PHE   ( 210-)  A      N    CA   C    97.30   -5.0
 255 VAL   ( 287-)  A      N    CA   C   124.63    4.8
 338 GLN   ( 370-)  A      N    CA   C    99.59   -4.1
 356 HIS   ( 388-)  A      NE2  CD2  CG  110.76    4.3
 376 LEU   ( 408-)  A      N    CA   C   125.33    5.0
 401 ARG   ( 433-)  A      CG   CD   NE  119.64    5.4
 401 ARG   ( 433-)  A      CD   NE   CZ  128.90    4.0
 667 TYR   ( 148-)  B      N    CA   C    98.10   -4.7
 674 VAL   ( 155-)  B      N    CA   C    99.84   -4.1
 723 HIS   ( 204-)  B      CG   ND1  CE1 109.65    4.0
 729 PHE   ( 210-)  B      N    CA   C    97.30   -5.0
 806 VAL   ( 287-)  B      N    CA   C   124.65    4.8
 889 GLN   ( 370-)  B      N    CA   C    99.57   -4.2
 907 HIS   ( 388-)  B      NE2  CD2  CG  110.73    4.2
 927 LEU   ( 408-)  B      N    CA   C   125.30    5.0
 952 ARG   ( 433-)  B      CG   CD   NE  119.65    5.4
 952 ARG   ( 433-)  B      CD   NE   CZ  128.91    4.0

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

 376 LEU   ( 408-)  A      CA    -6.6    24.05    34.19
 927 LEU   ( 408-)  B      CA    -6.6    24.04    34.19
The average deviation= 1.366

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.

 376 LEU   ( 408-)  A    5.70
 927 LEU   ( 408-)  B    5.69
 806 VAL   ( 287-)  B    5.64
 255 VAL   ( 287-)  A    5.64
1088 CYS   ( 569-)  B    5.46
 537 CYS   ( 569-)  A    5.45
 729 PHE   ( 210-)  B    5.37
 178 PHE   ( 210-)  A    5.37
 700 PHE   ( 181-)  B    5.01
 667 TYR   ( 148-)  B    5.00
 116 TYR   ( 148-)  A    5.00
 149 PHE   ( 181-)  A    4.98
 889 GLN   ( 370-)  B    4.63
 338 GLN   ( 370-)  A    4.63
 865 GLU   ( 346-)  B    4.55
 314 GLU   ( 346-)  A    4.54
 532 LEU   ( 564-)  A    4.12
1083 LEU   ( 564-)  B    4.12
 325 LEU   ( 357-)  A    4.11
 876 LEU   ( 357-)  B    4.10
  54 PRO   (  86-)  A    4.07
 605 PRO   (  86-)  B    4.06

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.725

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.

 655 TYR   ( 136-)  B      CB   4.25
 104 TYR   ( 136-)  A      CB   4.25
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.804

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.804

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.

 486 PHE   ( 518-)  A    -3.5
1037 PHE   ( 518-)  B    -3.5
 482 PRO   ( 514-)  A    -3.1
1033 PRO   ( 514-)  B    -3.1
1095 PRO   ( 576-)  B    -3.0
 544 PRO   ( 576-)  A    -3.0
 222 TYR   ( 254-)  A    -2.9
 773 TYR   ( 254-)  B    -2.9
  11 HIS   (  43-)  A    -2.6
 562 HIS   (  43-)  B    -2.6
 904 TYR   ( 385-)  B    -2.5
 353 TYR   ( 385-)  A    -2.5
 262 LEU   ( 294-)  A    -2.5
 813 LEU   ( 294-)  B    -2.5
 636 LEU   ( 117-)  B    -2.5
  85 LEU   ( 117-)  A    -2.5
 542 THR   ( 574-)  A    -2.4
1093 THR   ( 574-)  B    -2.4
 375 PHE   ( 407-)  A    -2.4
 926 PHE   ( 407-)  B    -2.4
1003 GLU   ( 484-)  B    -2.4
 452 GLU   ( 484-)  A    -2.4
 651 ILE   ( 132-)  B    -2.3
 100 ILE   ( 132-)  A    -2.3
 749 LEU   ( 230-)  B    -2.3
 198 LEU   ( 230-)  A    -2.3
 963 ILE   ( 444-)  B    -2.2
 412 ILE   ( 444-)  A    -2.2
 683 GLY   ( 164-)  B    -2.2
 132 GLY   ( 164-)  A    -2.2
 625 THR   ( 106-)  B    -2.2
  74 THR   ( 106-)  A    -2.2
 558 TYR   (  39-)  B    -2.2
   7 TYR   (  39-)  A    -2.2
 588 CYS   (  69-)  B    -2.1
  37 CYS   (  69-)  A    -2.1
 113 VAL   ( 145-)  A    -2.1
 664 VAL   ( 145-)  B    -2.1
 995 THR   ( 476-)  B    -2.1
 444 THR   ( 476-)  A    -2.1
 200 HIS   ( 232-)  A    -2.0
 117 THR   ( 149-)  A    -2.0
 668 THR   ( 149-)  B    -2.0
 344 ARG   ( 376-)  A    -2.0
 895 ARG   ( 376-)  B    -2.0
 751 HIS   ( 232-)  B    -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 GLN   (  44-)  A  Poor phi/psi
  21 ASP   (  53-)  A  Poor phi/psi
  22 ARG   (  54-)  A  Poor phi/psi
  37 CYS   (  69-)  A  Poor phi/psi
  94 SER   ( 126-)  A  PRO omega poor
  97 THR   ( 129-)  A  Poor phi/psi
 194 HIS   ( 226-)  A  Poor phi/psi
 198 LEU   ( 230-)  A  Poor phi/psi
 215 PHE   ( 247-)  A  Poor phi/psi
 217 ASP   ( 249-)  A  Poor phi/psi
 255 VAL   ( 287-)  A  Poor phi/psi
 263 LEU   ( 295-)  A  Poor phi/psi
 293 ASP   ( 325-)  A  Poor phi/psi
 380 SER   ( 412-)  A  Poor phi/psi
 454 GLU   ( 486-)  A  Poor phi/psi
 482 PRO   ( 514-)  A  Poor phi/psi
 513 TRP   ( 545-)  A  Poor phi/psi
 522 VAL   ( 554-)  A  Poor phi/psi
 547 SER   ( 579-)  A  Poor phi/psi
 563 GLN   (  44-)  B  Poor phi/psi
 572 ASP   (  53-)  B  Poor phi/psi
 573 ARG   (  54-)  B  Poor phi/psi
 588 CYS   (  69-)  B  Poor phi/psi
 645 SER   ( 126-)  B  PRO omega poor
 648 THR   ( 129-)  B  Poor phi/psi
 745 HIS   ( 226-)  B  Poor phi/psi
 749 LEU   ( 230-)  B  Poor phi/psi
 766 PHE   ( 247-)  B  Poor phi/psi
 768 ASP   ( 249-)  B  Poor phi/psi
 806 VAL   ( 287-)  B  Poor phi/psi
 814 LEU   ( 295-)  B  Poor phi/psi
 844 ASP   ( 325-)  B  Poor phi/psi
 931 SER   ( 412-)  B  Poor phi/psi
1005 GLU   ( 486-)  B  Poor phi/psi
1033 PRO   ( 514-)  B  Poor phi/psi
1064 TRP   ( 545-)  B  Poor phi/psi
1073 VAL   ( 554-)  B  Poor phi/psi
1098 SER   ( 579-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.488

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

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

chi-1/chi-2 correlation Z-score : -4.488

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.

 146 SER   ( 178-)  A    0.36
 697 SER   ( 178-)  B    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!

   4 CYS   (  36-)  A      0
   5 CYS   (  37-)  A      0
   7 TYR   (  39-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  11 HIS   (  43-)  A      0
  12 GLN   (  44-)  A      0
  20 LEU   (  52-)  A      0
  21 ASP   (  53-)  A      0
  22 ARG   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  33 SER   (  65-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  42 ILE   (  74-)  A      0
  51 ARG   (  83-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  73 ALA   ( 105-)  A      0
  91 LEU   ( 123-)  A      0
  93 PRO   ( 125-)  A      0
And so on for a total of 420 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 : 1.396

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!

 130 PRO   ( 162-)  A   1.83   11
 681 PRO   ( 162-)  B   1.83   11

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]

  40 PRO   (  72-)  A    0.46 HIGH
  93 PRO   ( 125-)  A    0.46 HIGH
  95 PRO   ( 127-)  A    0.45 HIGH
 232 PRO   ( 264-)  A    0.46 HIGH
 360 PRO   ( 392-)  A    0.45 HIGH
 367 PRO   ( 399-)  A    0.45 HIGH
 430 PRO   ( 462-)  A    0.46 HIGH
 506 PRO   ( 538-)  A    0.45 HIGH
 510 PRO   ( 542-)  A    0.46 HIGH
 591 PRO   (  72-)  B    0.46 HIGH
 644 PRO   ( 125-)  B    0.46 HIGH
 646 PRO   ( 127-)  B    0.45 HIGH
 783 PRO   ( 264-)  B    0.46 HIGH
 911 PRO   ( 392-)  B    0.45 HIGH
 918 PRO   ( 399-)  B    0.45 HIGH
 981 PRO   ( 462-)  B    0.46 HIGH
1057 PRO   ( 538-)  B    0.45 HIGH
1061 PRO   ( 542-)  B    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].

  35 PRO   (  67-)  A    50.2 half-chair C-delta/C-gamma (54 degrees)
 121 PRO   ( 153-)  A  -113.3 envelop C-gamma (-108 degrees)
 124 PRO   ( 156-)  A  -115.4 envelop C-gamma (-108 degrees)
 140 PRO   ( 172-)  A   106.5 envelop C-beta (108 degrees)
 244 PRO   ( 276-)  A  -120.2 half-chair C-delta/C-gamma (-126 degrees)
 264 PRO   ( 296-)  A  -119.1 half-chair C-delta/C-gamma (-126 degrees)
 357 PRO   ( 389-)  A  -133.1 half-chair C-delta/C-gamma (-126 degrees)
 398 PRO   ( 430-)  A    47.8 half-chair C-delta/C-gamma (54 degrees)
 482 PRO   ( 514-)  A   134.7 half-chair C-beta/C-alpha (126 degrees)
 586 PRO   (  67-)  B    50.2 half-chair C-delta/C-gamma (54 degrees)
 672 PRO   ( 153-)  B  -113.3 envelop C-gamma (-108 degrees)
 675 PRO   ( 156-)  B  -115.4 envelop C-gamma (-108 degrees)
 691 PRO   ( 172-)  B   106.5 envelop C-beta (108 degrees)
 795 PRO   ( 276-)  B  -120.1 half-chair C-delta/C-gamma (-126 degrees)
 815 PRO   ( 296-)  B  -119.1 half-chair C-delta/C-gamma (-126 degrees)
 908 PRO   ( 389-)  B  -133.0 half-chair C-delta/C-gamma (-126 degrees)
 949 PRO   ( 430-)  B    47.8 half-chair C-delta/C-gamma (54 degrees)
1033 PRO   ( 514-)  B   134.8 half-chair C-beta/C-alpha (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.

 675 PRO   ( 156-)  B      CG  <->  678 CYS   ( 159-)  B      SG     0.64    2.76  INTRA BL
 124 PRO   ( 156-)  A      CG  <->  127 CYS   ( 159-)  A      SG     0.64    2.76  INTRA BL
 356 HIS   ( 388-)  A      NE2 <-> 1113 HEM   ( 601-)  A      NC     0.40    2.60  INTRA BL
 907 HIS   ( 388-)  B      NE2 <-> 1114 HEM   ( 602-)  B      NC     0.40    2.60  INTRA BL
  99 ASN   ( 131-)  A      ND2 <->  102 HIS   ( 134-)  A      N      0.31    2.54  INTRA BL
 650 ASN   ( 131-)  B      ND2 <->  653 HIS   ( 134-)  B      N      0.31    2.54  INTRA BL
 222 TYR   ( 254-)  A      CD2 <->  278 ASN   ( 310-)  A      ND2    0.31    2.79  INTRA
 773 TYR   ( 254-)  B      CD2 <->  829 ASN   ( 310-)  B      ND2    0.31    2.79  INTRA
 448 GLU   ( 480-)  A      O   <->  479 LYS   ( 511-)  A      NZ     0.27    2.43  INTRA
 999 GLU   ( 480-)  B      O   <-> 1030 LYS   ( 511-)  B      NZ     0.27    2.43  INTRA
 356 HIS   ( 388-)  A      NE2 <-> 1113 HEM   ( 601-)  A      NB     0.26    2.74  INTRA BL
 907 HIS   ( 388-)  B      NE2 <-> 1114 HEM   ( 602-)  B      NB     0.26    2.74  INTRA BL
 615 GLY   (  96-)  B      O   <->  618 LEU   (  99-)  B      N      0.25    2.45  INTRA BL
  64 GLY   (  96-)  A      O   <->   67 LEU   (  99-)  A      N      0.25    2.45  INTRA BL
 610 PHE   (  91-)  B      CE1 <->  614 HIS   (  95-)  B      CD2    0.23    2.97  INTRA
  59 PHE   (  91-)  A      CE1 <->   63 HIS   (  95-)  A      CD2    0.23    2.97  INTRA
 247 ILE   ( 279-)  A      O   <->  252 GLN   ( 284-)  A      NE2    0.22    2.48  INTRA BF
 798 ILE   ( 279-)  B      O   <->  803 GLN   ( 284-)  B      NE2    0.22    2.48  INTRA BF
 810 VAL   ( 291-)  B      O   <->  812 GLY   ( 293-)  B      N      0.21    2.49  INTRA
 259 VAL   ( 291-)  A      O   <->  261 GLY   ( 293-)  A      N      0.21    2.49  INTRA
 764 ARG   ( 245-)  B      NH1 <->  848 PHE   ( 329-)  B      CD2    0.21    2.89  INTRA BL
 213 ARG   ( 245-)  A      NH1 <->  297 PHE   ( 329-)  A      CD2    0.21    2.89  INTRA BL
 711 GLN   ( 192-)  B      OE1 <-> 1036 ILE   ( 517-)  B      N      0.21    2.49  INTRA
 160 GLN   ( 192-)  A      OE1 <->  485 ILE   ( 517-)  A      N      0.21    2.49  INTRA
 403 GLY   ( 435-)  A      C   <->  480 CYS   ( 512-)  A      SG     0.20    3.20  INTRA
And so on for a total of 286 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

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.

 245 ARG   ( 277-)  A      -7.76
 796 ARG   ( 277-)  B      -7.76
 138 GLN   ( 170-)  A      -6.78
 689 GLN   ( 170-)  B      -6.78
  29 ARG   (  61-)  A      -6.71
 580 ARG   (  61-)  B      -6.67
 153 ARG   ( 185-)  A      -6.40
 704 ARG   ( 185-)  B      -6.37
 893 ARG   ( 374-)  B      -6.14
 342 ARG   ( 374-)  A      -6.13
 734 LYS   ( 215-)  B      -6.07
 183 LYS   ( 215-)  A      -6.05
 571 LEU   (  52-)  B      -5.36
  20 LEU   (  52-)  A      -5.36
 947 ARG   ( 428-)  B      -5.29
 396 ARG   ( 428-)  A      -5.29
1092 LYS   ( 573-)  B      -5.29
 541 LYS   ( 573-)  A      -5.29
 699 ARG   ( 180-)  B      -5.22
 148 ARG   ( 180-)  A      -5.21
 988 ARG   ( 469-)  B      -5.20
 437 ARG   ( 469-)  A      -5.20
 688 LYS   ( 169-)  B      -5.17
 137 LYS   ( 169-)  A      -5.17
 411 HIS   ( 443-)  A      -5.09
 962 HIS   ( 443-)  B      -5.08
 401 ARG   ( 433-)  A      -5.06
 155 PHE   ( 187-)  A      -5.05
 706 PHE   ( 187-)  B      -5.05
 952 ARG   ( 433-)  B      -5.05

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.

 137 LYS   ( 169-)  A       139 - LEU    171- ( A)         -5.54
 152 ARG   ( 184-)  A       155 - PHE    187- ( A)         -4.93
 688 LYS   ( 169-)  B       690 - LEU    171- ( B)         -5.54
 703 ARG   ( 184-)  B       706 - PHE    187- ( B)         -4.92

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

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.

 558 TYR   (  39-)  B   -2.73
   7 TYR   (  39-)  A   -2.72
 333 LEU   ( 365-)  A   -2.59
 884 LEU   ( 365-)  B   -2.59
 412 ILE   ( 444-)  A   -2.57
 963 ILE   ( 444-)  B   -2.57
 655 TYR   ( 136-)  B   -2.52
 104 TYR   ( 136-)  A   -2.51

Warning: Abnormal packing Z-score for sequential residues

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

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

 332 GLU   ( 364-)  A     -  335 PHE   ( 367-)  A        -2.00
 883 GLU   ( 364-)  B     -  886 PHE   ( 367-)  B        -1.93

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

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.

  90 ASN   ( 122-)  A
 176 GLN   ( 208-)  A
 288 HIS   ( 320-)  A
 343 ASN   ( 375-)  A
 411 HIS   ( 443-)  A
 641 ASN   ( 122-)  B
 727 GLN   ( 208-)  B
 839 HIS   ( 320-)  B
 894 ASN   ( 375-)  B
 962 HIS   ( 443-)  B

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.

  21 ASP   (  53-)  A      N
  32 TYR   (  64-)  A      N
  36 ASN   (  68-)  A      N
  43 TRP   (  75-)  A      N
  88 ARG   ( 120-)  A      NE
  88 ARG   ( 120-)  A      NH2
  99 ASN   ( 131-)  A      ND2
 100 ILE   ( 132-)  A      N
 101 ALA   ( 133-)  A      N
 104 TYR   ( 136-)  A      N
 106 SER   ( 138-)  A      N
 107 TRP   ( 139-)  A      N
 118 ARG   ( 150-)  A      NE
 118 ARG   ( 150-)  A      NH1
 133 THR   ( 165-)  A      OG1
 148 ARG   ( 180-)  A      NE
 153 ARG   ( 185-)  A      NE
 171 GLN   ( 203-)  A      NE2
 172 HIS   ( 204-)  A      NE2
 176 GLN   ( 208-)  A      NE2
 181 SER   ( 213-)  A      OG
 189 THR   ( 221-)  A      OG1
 195 GLY   ( 227-)  A      N
 207 GLU   ( 239-)  A      N
 208 ARG   ( 240-)  A      NE
And so on for a total of 119 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.

  99 ASN   ( 131-)  A      OD1
 172 HIS   ( 204-)  A      ND1
 288 HIS   ( 320-)  A      ND1
 307 GLU   ( 339-)  A      OE1
 351 GLN   ( 383-)  A      OE1
 369 ASP   ( 401-)  A      OD1
 481 HIS   ( 513-)  A      ND1
 650 ASN   ( 131-)  B      OD1
 723 HIS   ( 204-)  B      ND1
 839 HIS   ( 320-)  B      ND1
 846 GLN   ( 327-)  B      OE1
 858 GLU   ( 339-)  B      OE1
 902 GLN   ( 383-)  B      OE1
 920 ASP   ( 401-)  B      OD1
1032 HIS   ( 513-)  B      ND1

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: 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.

 108 GLU   ( 140-)  A   H-bonding suggests Gln; but Alt-Rotamer
 384 ASP   ( 416-)  A   H-bonding suggests Asn
 659 GLU   ( 140-)  B   H-bonding suggests Gln; but Alt-Rotamer
 935 ASP   ( 416-)  B   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 :  -1.936
  2nd generation packing quality :  -2.193
  Ramachandran plot appearance   :  -3.804 (poor)
  chi-1/chi-2 rotamer normality  :  -4.488 (bad)
  Backbone conformation          :  -0.709

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.526 (tight)
  Bond angles                    :   0.811
  Omega angle restraints         :   0.254 (tight)
  Side chain planarity           :   0.565 (tight)
  Improper dihedral distribution :   1.115
  Inside/Outside distribution    :   1.098

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 3.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.526 (tight)
  Bond angles                    :   0.811
  Omega angle restraints         :   0.254 (tight)
  Side chain planarity           :   0.565 (tight)
  Improper dihedral distribution :   1.115
  Inside/Outside distribution    :   1.098
==============

WHAT IF
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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.