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 pdb1pgf.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: 128837.313
Volume of the Unit Cell V= 4819813.0
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= 4.676
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.550

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1111 IMM   ( 800-)  A  -         Fragmented
1112 HEM   ( 601-)  A  -         OK
1113 IMM   ( 800-)  B  -         Fragmented
1114 HEM   ( 601-)  B  -         OK

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: 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 : 12.68

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

 |  1.002705  0.000395  0.000273|
 |  0.000395  1.002257  0.000256|
 |  0.000273  0.000256  1.002089|
Proposed new scale matrix

 |  0.010052 -0.000004 -0.000003|
 | -0.000002  0.004774 -0.000001|
 | -0.000001 -0.000001  0.004293|
With corresponding cell

    A    =  99.485  B   = 209.458  C    = 232.936
    Alpha=  89.971  Beta=  89.969  Gamma=  89.955

The CRYST1 cell dimensions

    A    =  99.220  B   = 208.990  C    = 232.430
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 217.340
(Under-)estimated Z-score: 10.865

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.

  61 LEU   (  93-)  A      CA   CB   CG   98.84   -5.0
 102 HIS   ( 134-)  A      CG   ND1  CE1 109.63    4.0
 116 TYR   ( 148-)  A      N    CA   C    95.27   -5.7
 192 LEU   ( 224-)  A      N    CA   C    96.23   -5.3
 193 GLY   ( 225-)  A      N    CA   C    99.33   -4.5
 356 HIS   ( 388-)  A      NE2  CD2  CG  111.08    4.6
 376 LEU   ( 408-)  A      N    CA   C   127.95    6.0
 401 ARG   ( 433-)  A      CG   CD   NE  120.30    5.8
 401 ARG   ( 433-)  A      CD   NE   CZ  129.93    4.6
 537 CYS   ( 569-)  A      CA   CB   SG  105.12   -4.0
 549 HIS   ( 581-)  A      CG   ND1  CE1 109.80    4.2
 609 HIS   (  90-)  B      CG   ND1  CE1 109.64    4.0
 612 LEU   (  93-)  B      CA   CB   CG   98.80   -5.0
 653 HIS   ( 134-)  B      CG   ND1  CE1 109.66    4.1
 667 TYR   ( 148-)  B      N    CA   C    95.29   -5.7
 743 LEU   ( 224-)  B      N    CA   C    96.22   -5.3
 744 GLY   ( 225-)  B      N    CA   C    99.35   -4.5
 907 HIS   ( 388-)  B      NE2  CD2  CG  111.06    4.6
 927 LEU   ( 408-)  B      N    CA   C   128.01    6.0
 952 ARG   ( 433-)  B      CG   CD   NE  120.28    5.8
 952 ARG   ( 433-)  B      CD   NE   CZ  129.95    4.6
1088 CYS   ( 569-)  B      CA   CB   SG  105.10   -4.0
1100 HIS   ( 581-)  B      CG   ND1  CE1 109.80    4.2

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    -7.1    23.25    34.19
 927 LEU   ( 408-)  B      CA    -7.2    23.24    34.19
The average deviation= 1.471

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.

 927 LEU   ( 408-)  B    6.79
 376 LEU   ( 408-)  A    6.76
 743 LEU   ( 224-)  B    6.10
 192 LEU   ( 224-)  A    6.10
 116 TYR   ( 148-)  A    6.07
 667 TYR   ( 148-)  B    6.07
1077 LEU   ( 558-)  B    5.74
 526 LEU   ( 558-)  A    5.71
1039 GLU   ( 520-)  B    5.65
 488 GLU   ( 520-)  A    5.65
 449 LEU   ( 481-)  A    5.49
1000 LEU   ( 481-)  B    5.48
 640 SER   ( 121-)  B    5.38
  89 SER   ( 121-)  A    5.37
1049 SER   ( 530-)  B    5.29
 498 SER   ( 530-)  A    5.29
1044 MET   ( 525-)  B    5.25
 493 MET   ( 525-)  A    5.25
 865 GLU   ( 346-)  B    5.22
 314 GLU   ( 346-)  A    5.21
 193 GLY   ( 225-)  A    5.11
 744 GLY   ( 225-)  B    5.11
1088 CYS   ( 569-)  B    5.09
 537 CYS   ( 569-)  A    5.09
1010 LEU   ( 491-)  B    5.03
 459 LEU   ( 491-)  A    5.00
 149 PHE   ( 181-)  A    4.88
 700 PHE   ( 181-)  B    4.88
 313 ILE   ( 345-)  A    4.56
 864 ILE   ( 345-)  B    4.56
  54 PRO   (  86-)  A    4.42
 605 PRO   (  86-)  B    4.42
1079 LYS   ( 560-)  B    4.39
 528 LYS   ( 560-)  A    4.38
 268 LEU   ( 300-)  A    4.35
 806 VAL   ( 287-)  B    4.35
 466 ILE   ( 498-)  A    4.35
 819 LEU   ( 300-)  B    4.35
 255 VAL   ( 287-)  A    4.34
1017 ILE   ( 498-)  B    4.34
 178 PHE   ( 210-)  A    4.21
 729 PHE   ( 210-)  B    4.21
 545 TYR   ( 577-)  A    4.20
1096 TYR   ( 577-)  B    4.20
 220 LEU   ( 252-)  A    4.13
 771 LEU   ( 252-)  B    4.12
 847 LEU   ( 328-)  B    4.11
 889 GLN   ( 370-)  B    4.11
 296 LEU   ( 328-)  A    4.11
 338 GLN   ( 370-)  A    4.10

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 : 1.848

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.

 434 TYR   ( 466-)  A      CB   4.21
 985 TYR   ( 466-)  B      CB   4.21
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.679

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 : -3.679

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.

1037 PHE   ( 518-)  B    -3.5
 486 PHE   ( 518-)  A    -3.5
1033 PRO   ( 514-)  B    -3.1
 482 PRO   ( 514-)  A    -3.1
1082 THR   ( 563-)  B    -2.7
 531 THR   ( 563-)  A    -2.7
 766 PHE   ( 247-)  B    -2.5
 215 PHE   ( 247-)  A    -2.5
 222 TYR   ( 254-)  A    -2.5
 773 TYR   ( 254-)  B    -2.5
 757 LEU   ( 238-)  B    -2.5
 206 LEU   ( 238-)  A    -2.5
 177 PHE   ( 209-)  A    -2.4
 728 PHE   ( 209-)  B    -2.4
 749 LEU   ( 230-)  B    -2.4
1003 GLU   ( 484-)  B    -2.4
 452 GLU   ( 484-)  A    -2.4
 895 ARG   ( 376-)  B    -2.4
 198 LEU   ( 230-)  A    -2.4
  17 ARG   (  49-)  A    -2.4
 344 ARG   ( 376-)  A    -2.4
 568 ARG   (  49-)  B    -2.4
 100 ILE   ( 132-)  A    -2.3
 651 ILE   ( 132-)  B    -2.3
 329 PHE   ( 361-)  A    -2.3
And so on for a total of 74 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

  12 GLN   (  44-)  A  Poor phi/psi
  29 ARG   (  61-)  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
 198 LEU   ( 230-)  A  Poor phi/psi
 215 PHE   ( 247-)  A  Poor phi/psi
 217 ASP   ( 249-)  A  Poor phi/psi
 222 TYR   ( 254-)  A  Poor phi/psi
 226 ASN   ( 258-)  A  Poor phi/psi
 238 PRO   ( 270-)  A  Poor phi/psi
 255 VAL   ( 287-)  A  Poor phi/psi
 263 LEU   ( 295-)  A  Poor phi/psi
 341 TYR   ( 373-)  A  Poor phi/psi
 354 HIS   ( 386-)  A  Poor phi/psi
 355 TRP   ( 387-)  A  Poor phi/psi
 452 GLU   ( 484-)  A  Poor phi/psi
 471 PHE   ( 503-)  A  Poor phi/psi
 482 PRO   ( 514-)  A  Poor phi/psi
 488 GLU   ( 520-)  A  Poor phi/psi
 563 GLN   (  44-)  B  Poor phi/psi
 580 ARG   (  61-)  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
 749 LEU   ( 230-)  B  Poor phi/psi
 766 PHE   ( 247-)  B  Poor phi/psi
 768 ASP   ( 249-)  B  Poor phi/psi
 773 TYR   ( 254-)  B  Poor phi/psi
 777 ASN   ( 258-)  B  Poor phi/psi
 789 PRO   ( 270-)  B  Poor phi/psi
 806 VAL   ( 287-)  B  Poor phi/psi
 814 LEU   ( 295-)  B  Poor phi/psi
 892 TYR   ( 373-)  B  Poor phi/psi
 905 HIS   ( 386-)  B  Poor phi/psi
 906 TRP   ( 387-)  B  Poor phi/psi
1003 GLU   ( 484-)  B  Poor phi/psi
1022 PHE   ( 503-)  B  Poor phi/psi
1033 PRO   ( 514-)  B  Poor phi/psi
1039 GLU   ( 520-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.039

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 : -4.039

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.

 109 SER   ( 141-)  A    0.36
 660 SER   ( 141-)  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
   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
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 TYR   (  64-)  A      0
  33 SER   (  65-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  42 ILE   (  74-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  73 ALA   ( 105-)  A      0
  93 PRO   ( 125-)  A      0
  94 SER   ( 126-)  A      0
  95 PRO   ( 127-)  A      0
  96 PRO   ( 128-)  A      0
And so on for a total of 419 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 : 1.642

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   1.61   10
 681 PRO   ( 162-)  B   1.61   10

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
 264 PRO   ( 296-)  A    0.45 HIGH
 360 PRO   ( 392-)  A    0.45 HIGH
 544 PRO   ( 576-)  A    0.45 HIGH
 591 PRO   (  72-)  B    0.46 HIGH
 815 PRO   ( 296-)  B    0.45 HIGH
 911 PRO   ( 392-)  B    0.45 HIGH
1095 PRO   ( 576-)  B    0.45 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].

 159 PRO   ( 191-)  A  -116.3 envelop C-gamma (-108 degrees)
 482 PRO   ( 514-)  A   135.3 envelop C-alpha (144 degrees)
 710 PRO   ( 191-)  B  -116.3 envelop C-gamma (-108 degrees)
1033 PRO   ( 514-)  B   135.2 envelop C-alpha (144 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.

 642 LEU   ( 123-)  B      O   <->  988 ARG   ( 469-)  B      NH2    0.42    2.28  INTRA BL
  91 LEU   ( 123-)  A      O   <->  437 ARG   ( 469-)  A      NH2    0.42    2.28  INTRA BL
 907 HIS   ( 388-)  B      NE2 <-> 1114 HEM   ( 601-)  B      NA     0.38    2.62  INTRA BL
 356 HIS   ( 388-)  A      NE2 <-> 1112 HEM   ( 601-)  A      NA     0.38    2.62  INTRA BL
 699 ARG   ( 180-)  B      NH1 <-> 1009 GLU   ( 490-)  B      OE1    0.30    2.40  INTRA
 148 ARG   ( 180-)  A      NH1 <->  458 GLU   ( 490-)  A      OE1    0.30    2.40  INTRA
 118 ARG   ( 150-)  A      NH2 <->  426 LEU   ( 458-)  A      O      0.29    2.41  INTRA BL
 669 ARG   ( 150-)  B      NH2 <->  977 LEU   ( 458-)  B      O      0.28    2.42  INTRA BL
 356 HIS   ( 388-)  A      N   <->  357 PRO   ( 389-)  A      CD     0.28    2.72  INTRA BL
 907 HIS   ( 388-)  B      N   <->  908 PRO   ( 389-)  B      CD     0.28    2.72  INTRA BL
 906 TRP   ( 387-)  B      NE1 <-> 1041 MET   ( 522-)  B      CE     0.27    2.83  INTRA BL
 355 TRP   ( 387-)  A      NE1 <->  490 MET   ( 522-)  A      CE     0.27    2.83  INTRA BL
 481 HIS   ( 513-)  A      CE1 <->  488 GLU   ( 520-)  A      N      0.27    2.83  INTRA
1032 HIS   ( 513-)  B      CE1 <-> 1039 GLU   ( 520-)  B      N      0.27    2.83  INTRA
 356 HIS   ( 388-)  A      NE2 <-> 1112 HEM   ( 601-)  A      NB     0.27    2.73  INTRA BL
 907 HIS   ( 388-)  B      NE2 <-> 1114 HEM   ( 601-)  B      NB     0.27    2.73  INTRA BL
1075 PHE   ( 556-)  B      CE2 <-> 1079 LYS   ( 560-)  B      NZ     0.26    2.84  INTRA
 524 PHE   ( 556-)  A      CE2 <->  528 LYS   ( 560-)  A      NZ     0.26    2.84  INTRA
 874 TYR   ( 355-)  B      CE2 <-> 1113 IMM   ( 800-)  B      C20    0.24    2.96  INTRA BL
 323 TYR   ( 355-)  A      CE2 <-> 1111 IMM   ( 800-)  A      C20    0.24    2.96  INTRA BL
 354 HIS   ( 386-)  A      NE2 <-> 1112 HEM   ( 601-)  A      CAD    0.23    2.87  INTRA BL
 905 HIS   ( 386-)  B      NE2 <-> 1114 HEM   ( 601-)  B      CAD    0.23    2.87  INTRA BL
 989 PHE   ( 470-)  B      CZ  <-> 1048 PHE   ( 529-)  B      CE2    0.21    2.99  INTRA BL
 438 PHE   ( 470-)  A      CZ  <->  497 PHE   ( 529-)  A      CE2    0.21    2.99  INTRA BL
 338 GLN   ( 370-)  A      NE2 <->  888 ALA   ( 369-)  B      O      0.20    2.50  INTRA
And so on for a total of 330 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      -7.87
 796 ARG   ( 277-)  B      -7.87
  29 ARG   (  61-)  A      -6.82
 580 ARG   (  61-)  B      -6.81
 689 GLN   ( 170-)  B      -6.28
 138 GLN   ( 170-)  A      -6.26
 893 ARG   ( 374-)  B      -6.07
 183 LYS   ( 215-)  A      -6.06
 734 LYS   ( 215-)  B      -6.06
 342 ARG   ( 374-)  A      -6.03
 571 LEU   (  52-)  B      -5.76
  20 LEU   (  52-)  A      -5.74
 704 ARG   ( 185-)  B      -5.54
 153 ARG   ( 185-)  A      -5.54
 947 ARG   ( 428-)  B      -5.39
 396 ARG   ( 428-)  A      -5.39
 155 PHE   ( 187-)  A      -5.34
 706 PHE   ( 187-)  B      -5.34
 962 HIS   ( 443-)  B      -5.32
 411 HIS   ( 443-)  A      -5.32
 541 LYS   ( 573-)  A      -5.30
1092 LYS   ( 573-)  B      -5.30
 889 GLN   ( 370-)  B      -5.13
 952 ARG   ( 433-)  B      -5.12
 401 ARG   ( 433-)  A      -5.12
 988 ARG   ( 469-)  B      -5.11
 437 ARG   ( 469-)  A      -5.11
 148 ARG   ( 180-)  A      -5.08
 699 ARG   ( 180-)  B      -5.08
 682 MET   ( 163-)  B      -5.07
 338 GLN   ( 370-)  A      -5.03
 131 MET   ( 163-)  A      -5.02

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)         -5.30
 153 ARG   ( 185-)  A       155 - PHE    187- ( A)         -5.05
 688 LYS   ( 169-)  B       690 - LEU    171- ( B)         -5.30
 704 ARG   ( 185-)  B       706 - PHE    187- ( B)         -5.05

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.

   7 TYR   (  39-)  A   -2.60
 558 TYR   (  39-)  B   -2.60
 963 ILE   ( 444-)  B   -2.59
 412 ILE   ( 444-)  A   -2.59
 884 LEU   ( 365-)  B   -2.52

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

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.

  10 GLN   (  42-)  A
 102 HIS   ( 134-)  A
 194 HIS   ( 226-)  A
 343 ASN   ( 375-)  A
 411 HIS   ( 443-)  A
 447 GLN   ( 479-)  A
 561 GLN   (  42-)  B
 653 HIS   ( 134-)  B
 745 HIS   ( 226-)  B
 894 ASN   ( 375-)  B
 962 HIS   ( 443-)  B
 998 GLN   ( 479-)  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.

  17 ARG   (  49-)  A      NH1
  36 ASN   (  68-)  A      N
  43 TRP   (  75-)  A      N
  99 ASN   ( 131-)  A      ND2
 100 ILE   ( 132-)  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
 119 ILE   ( 151-)  A      N
 131 MET   ( 163-)  A      N
 153 ARG   ( 185-)  A      NE
 153 ARG   ( 185-)  A      NH2
 171 GLN   ( 203-)  A      NE2
 172 HIS   ( 204-)  A      NE2
 176 GLN   ( 208-)  A      NE2
 181 SER   ( 213-)  A      OG
 198 LEU   ( 230-)  A      N
 207 GLU   ( 239-)  A      N
 208 ARG   ( 240-)  A      NE
 208 ARG   ( 240-)  A      NH2
 213 ARG   ( 245-)  A      NE
 213 ARG   ( 245-)  A      NH1
 215 PHE   ( 247-)  A      N
And so on for a total of 111 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.

 172 HIS   ( 204-)  A      ND1
 176 GLN   ( 208-)  A      OE1
 288 HIS   ( 320-)  A      NE2
 307 GLU   ( 339-)  A      OE1
 351 GLN   ( 383-)  A      OE1
 481 HIS   ( 513-)  A      ND1
 723 HIS   ( 204-)  B      ND1
 727 GLN   ( 208-)  B      OE1
 839 HIS   ( 320-)  B      NE2
 858 GLU   ( 339-)  B      OE1
 901 ASN   ( 382-)  B      OD1
 902 GLN   ( 383-)  B      OE1
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
 478 GLU   ( 510-)  A   H-bonding suggests Gln
 659 GLU   ( 140-)  B   H-bonding suggests Gln; but Alt-Rotamer
 935 ASP   ( 416-)  B   H-bonding suggests Asn
1029 GLU   ( 510-)  B   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 :  -1.942
  2nd generation packing quality :  -2.029
  Ramachandran plot appearance   :  -3.679 (poor)
  chi-1/chi-2 rotamer normality  :  -4.039 (bad)
  Backbone conformation          :  -0.983

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.612 (tight)
  Bond angles                    :   0.873
  Omega angle restraints         :   0.298 (tight)
  Side chain planarity           :   0.667
  Improper dihedral distribution :   1.208
  Inside/Outside distribution    :   1.100

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 : 4.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.612 (tight)
  Bond angles                    :   0.873
  Omega angle restraints         :   0.298 (tight)
  Side chain planarity           :   0.667
  Improper dihedral distribution :   1.208
  Inside/Outside distribution    :   1.100
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      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,
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    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.