WHAT IF Check report

This file was created 2012-01-31 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 pdb2qcu.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 113.791  B   = 114.097  C    = 192.801
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 113.791  B   = 114.097  C    = 125.637
    Alpha= 117.005  Beta= 116.927  Gamma=  90.000

Dimensions of the conventional cell

    A    = 114.097  B   = 113.791  C    = 192.801
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  1.000000  0.000000|
 | -1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: I 2 2 2

Bravais type of conventional cell is: I

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 : 0.854
CA-only RMS fit for the two chains : 0.513

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

Warning: New symmetry found

In the conventional cell, independent molecules in the asymmetric unit seemingly become symmetry relatives. This fact needs manual checking.

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.

1003 FAD   ( 600-)  A  -
1004 BOG   ( 700-)  A  -
1005 TAM   ( 805-)  A  -
1006 BOG   ( 701-)  A  -
1007 BOG   ( 700-)  B  -
1008 BOG   ( 800-)  A  -
1011 IMD   ( 807-)  A  -
1022 BOG   ( 801-)  A  -
1028 TAM   ( 823-)  A  -
1048 TAM   ( 810-)  B  -
1049 BOG   ( 800-)  B  -
1050 IMD   ( 821-)  A  -
1051 FAD   ( 600-)  B  -

Administrative problems that can generate validation failures

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

  35 LEU   (  37-)  A  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: 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.

 284 GLU   ( 286-)  A
 584 MET   (  85-)  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.

  77 PRO   (  79-)  A    Zero
 155 GLN   ( 157-)  A    Zero
 311 TYR   ( 313-)  A    Zero
 954 VAL   ( 455-)  B    Zero
1000 SER   ( 501-)  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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 252 ARG   ( 254-)  A
 393 ARG   ( 395-)  A
 467 ARG   ( 469-)  A

Warning: Tyrosine convention problem

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

 193 TYR   ( 195-)  A
 294 TYR   ( 296-)  A
 356 TYR   ( 358-)  A
 445 TYR   ( 447-)  A
 558 TYR   (  59-)  B
 790 TYR   ( 291-)  B
 812 TYR   ( 313-)  B
 857 TYR   ( 358-)  B
 946 TYR   ( 447-)  B

Warning: Phenylalanine convention problem

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

  81 PHE   (  83-)  A
 104 PHE   ( 106-)  A
 123 PHE   ( 125-)  A
 137 PHE   ( 139-)  A
 406 PHE   ( 408-)  A
 582 PHE   (  83-)  B
 605 PHE   ( 106-)  B
 638 PHE   ( 139-)  B
 756 PHE   ( 257-)  B
 799 PHE   ( 300-)  B

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.

 186 ASP   ( 188-)  A
 276 ASP   ( 278-)  A
 394 ASP   ( 396-)  A
 454 ASP   ( 456-)  A
 520 ASP   (  21-)  B
 687 ASP   ( 188-)  B

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.

 183 GLU   ( 185-)  A
 185 GLU   ( 187-)  A
 339 GLU   ( 341-)  A
 381 GLU   ( 383-)  A
 390 GLU   ( 392-)  A
 456 GLU   ( 458-)  A
 559 GLU   (  60-)  B
 565 GLU   (  66-)  B
 639 GLU   ( 140-)  B
 684 GLU   ( 185-)  B
 686 GLU   ( 187-)  B
 763 GLU   ( 264-)  B
 840 GLU   ( 341-)  B
 862 GLU   ( 363-)  B
 891 GLU   ( 392-)  B
 939 GLU   ( 440-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.516
RMS-deviation in bond distances: 0.012

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

 |  0.996882 -0.002050  0.000604|
 | -0.002050  0.996096  0.000452|
 |  0.000604  0.000452  0.998203|
Proposed new scale matrix

 |  0.008816  0.000018 -0.000005|
 |  0.000018  0.008798 -0.000004|
 | -0.000003 -0.000002  0.005196|
With corresponding cell

    A    = 113.437  B   = 113.658  C    = 192.443
    Alpha=  89.948  Beta=  89.931  Gamma=  90.236

The CRYST1 cell dimensions

    A    = 113.791  B   = 114.097  C    = 192.801
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 354.842
(Under-)estimated Z-score: 13.883

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.

  48 HIS   (  50-)  A      N    CA   C   124.49    4.7
 238 HIS   ( 240-)  A      CG   ND1  CE1 109.66    4.1
 442 HIS   ( 444-)  A      CG   ND1  CE1 109.75    4.2
 501 GLU   (   2-)  B      N    CA   C    95.63   -5.6
 549 HIS   (  50-)  B      N    CA   C   125.20    5.0
 636 ARG   ( 137-)  B      CG   CD   NE  117.36    4.0
 732 HIS   ( 233-)  B      CG   ND1  CE1 109.71    4.1
 897 TYR   ( 398-)  B     -C    N    CA  112.37   -5.2
 919 THR   ( 420-)  B      CA   CB   OG1 117.80    5.5
 919 THR   ( 420-)  B      CG2  CB   OG1 119.66    5.2

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.

 183 GLU   ( 185-)  A
 185 GLU   ( 187-)  A
 186 ASP   ( 188-)  A
 252 ARG   ( 254-)  A
 276 ASP   ( 278-)  A
 339 GLU   ( 341-)  A
 381 GLU   ( 383-)  A
 390 GLU   ( 392-)  A
 393 ARG   ( 395-)  A
 394 ASP   ( 396-)  A
 454 ASP   ( 456-)  A
 456 GLU   ( 458-)  A
 467 ARG   ( 469-)  A
 520 ASP   (  21-)  B
 559 GLU   (  60-)  B
 565 GLU   (  66-)  B
 639 GLU   ( 140-)  B
 684 GLU   ( 185-)  B
 686 GLU   ( 187-)  B
 687 ASP   ( 188-)  B
 763 GLU   ( 264-)  B
 840 GLU   ( 341-)  B
 862 GLU   ( 363-)  B
 891 GLU   ( 392-)  B
 939 GLU   ( 440-)  B

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  48 HIS   (  50-)  A      CA   -10.5    14.86    34.11
 267 GLY   ( 269-)  A      C     -8.3   -10.94     0.06
 314 VAL   ( 316-)  A      C     -7.4    -9.92     0.15
 508 ILE   (   9-)  B      C     -6.8    -8.83     0.03
 549 HIS   (  50-)  B      CA   -10.1    15.48    34.11
 589 PRO   (  90-)  B      C     -6.6   -10.06     0.42
 700 GLY   ( 201-)  B      C     -6.1    -8.03     0.06
 703 ASN   ( 204-)  B      C     -6.6   -10.14     0.27
 725 ILE   ( 226-)  B      CA    -6.1    24.03    33.24
 815 VAL   ( 316-)  B      C     -8.1   -10.94     0.15
 912 LEU   ( 413-)  B      CG    13.4    -9.43   -33.01
 919 THR   ( 420-)  B      CB    -8.2    15.62    34.09
The average deviation= 1.869

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.

 501 GLU   (   2-)  B    5.40
 549 HIS   (  50-)  B    4.52
  48 HIS   (  50-)  A    4.29
 725 ILE   ( 226-)  B    4.19
 327 ALA   ( 329-)  A    4.15

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 956 HIS   ( 457-)  B   10.43
 972 GLN   ( 473-)  B    9.22
 686 GLU   ( 187-)  B    8.06
 448 GLU   ( 450-)  A    7.41
 771 ASP   ( 272-)  B    7.02
 647 ASP   ( 148-)  B    6.83
 186 ASP   ( 188-)  A    6.66
 455 HIS   ( 457-)  A    6.36
 270 ASP   ( 272-)  A    6.32
 793 ASN   ( 294-)  B    6.04
 210 GLN   ( 212-)  A    5.71
 138 GLU   ( 140-)  A    5.21
 146 ASP   ( 148-)  A    5.06
 163 GLU   ( 165-)  A    4.82
 414 HIS   ( 416-)  A    4.43
 443 GLU   ( 445-)  A    4.30
 923 ASN   ( 424-)  B    4.18
 535 ASP   (  36-)  B    4.15
 311 TYR   ( 313-)  A    4.12
 656 GLN   ( 157-)  B    4.11
 422 ASN   ( 424-)  A    4.06

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.

 995 ARG   ( 496-)  B    -3.0
 268 THR   ( 270-)  A    -2.8
 558 TYR   (  59-)  B    -2.8
  57 TYR   (  59-)  A    -2.7
 564 SER   (  65-)  B    -2.7
 725 ILE   ( 226-)  B    -2.7
 613 ARG   ( 114-)  B    -2.6
 943 HIS   ( 444-)  B    -2.6
 390 GLU   ( 392-)  A    -2.6
 891 GLU   ( 392-)  B    -2.5
 636 ARG   ( 137-)  B    -2.5
 831 ARG   ( 332-)  B    -2.5
 494 ARG   ( 496-)  A    -2.5
 112 ARG   ( 114-)  A    -2.4
 119 THR   ( 121-)  A    -2.4
 134 LYS   ( 136-)  A    -2.3
 612 LYS   ( 113-)  B    -2.3
 493 GLN   ( 495-)  A    -2.2
 610 LEU   ( 111-)  B    -2.2
 251 LYS   ( 253-)  A    -2.2
 779 LYS   ( 280-)  B    -2.2
 892 GLY   ( 393-)  B    -2.2
 994 GLN   ( 495-)  B    -2.2
 552 LEU   (  53-)  B    -2.1
 339 GLU   ( 341-)  A    -2.1
 274 LYS   ( 276-)  A    -2.1
 330 ARG   ( 332-)  A    -2.1
 896 ASP   ( 397-)  B    -2.1
 997 SER   ( 498-)  B    -2.1
 239 THR   ( 241-)  A    -2.1
 224 ILE   ( 226-)  A    -2.0
 109 LEU   ( 111-)  A    -2.0
 108 HIS   ( 110-)  A    -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.

   9 GLY   (  11-)  A  omega poor
  33 GLN   (  35-)  A  Poor phi/psi
  36 ALA   (  38-)  A  Poor phi/psi
  38 ALA   (  40-)  A  Poor phi/psi
  45 LYS   (  47-)  A  Poor phi/psi
  47 ILE   (  49-)  A  omega poor
  48 HIS   (  50-)  A  omega poor
  57 TYR   (  59-)  A  Poor phi/psi
  58 GLU   (  60-)  A  Poor phi/psi
 102 GLY   ( 104-)  A  Poor phi/psi
 110 GLY   ( 112-)  A  Poor phi/psi
 111 LYS   ( 113-)  A  Poor phi/psi
 112 ARG   ( 114-)  A  Poor phi/psi
 113 THR   ( 115-)  A  omega poor
 114 SER   ( 116-)  A  Poor phi/psi
 117 GLY   ( 119-)  A  omega poor
 118 SER   ( 120-)  A  Poor phi/psi
 121 LEU   ( 123-)  A  omega poor
 140 SER   ( 142-)  A  omega poor
 141 ASP   ( 143-)  A  Poor phi/psi
 177 ASN   ( 179-)  A  Poor phi/psi
 180 TRP   ( 182-)  A  omega poor
 215 GLY   ( 217-)  A  omega poor
 251 LYS   ( 253-)  A  Poor phi/psi
 256 VAL   ( 258-)  A  omega poor
And so on for a total of 101 lines.

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.

  63 SER   (  65-)  A    0.35
 569 GLU   (  70-)  B    0.36
 620 THR   ( 121-)  B    0.36
 911 SER   ( 412-)  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!

   7 ILE   (   9-)  A      0
  11 ILE   (  13-)  A      0
  33 GLN   (  35-)  A      0
  34 ASP   (  36-)  A      0
  35 LEU   (  37-)  A      0
  36 ALA   (  38-)  A      0
  37 CYS   (  39-)  A      0
  38 ALA   (  40-)  A      0
  39 THR   (  41-)  A      0
  44 SER   (  46-)  A      0
  48 HIS   (  50-)  A      0
  57 TYR   (  59-)  A      0
  58 GLU   (  60-)  A      0
  76 ALA   (  78-)  A      0
  80 ALA   (  82-)  A      0
  82 PRO   (  84-)  A      0
  89 HIS   (  91-)  A      0
  94 ARG   (  96-)  A      0
 108 HIS   ( 110-)  A      0
 109 LEU   ( 111-)  A      0
 111 LYS   ( 113-)  A      0
 112 ARG   ( 114-)  A      0
 114 SER   ( 116-)  A      0
 118 SER   ( 120-)  A      0
 128 VAL   ( 130-)  A      0
And so on for a total of 405 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 8.251

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!

 724 GLY   ( 225-)  B   3.59   17
 117 GLY   ( 119-)  A   3.41   29
 351 GLY   ( 353-)  A   1.80   27
 852 GLY   ( 353-)  B   1.65   32

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]

  91 PRO   (  93-)  A    0.19 LOW
 258 PRO   ( 260-)  A    0.08 LOW
 316 PRO   ( 318-)  A    0.15 LOW
 759 PRO   ( 260-)  B    0.13 LOW
 817 PRO   ( 318-)  B    0.16 LOW

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].

 906 PRO   ( 407-)  B    48.8 half-chair C-delta/C-gamma (54 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.

  49 GLY   (  51-)  A      CA  <->   66 LEU   (  68-)  A      CD1    0.84    2.36  INTRA BF
 394 ASP   ( 396-)  A      N   <->  395 ASP   ( 397-)  A      CA     0.79    2.11  INTRA BF
 613 ARG   ( 114-)  B      NH2 <->  618 GLY   ( 119-)  B      CA     0.71    2.39  INTRA BF
 393 ARG   ( 395-)  A      CB  <->  394 ASP   ( 396-)  A      CB     0.70    2.30  INTRA BF
 894 ARG   ( 395-)  B      CD  <->  918 ARG   ( 419-)  B      NH2    0.66    2.44  INTRA BF
 271 VAL   ( 273-)  A      CG2 <-> 1028 TAM   ( 823-)  A      C3     0.62    2.58  INTRA
 393 ARG   ( 395-)  A      N   <->  394 ASP   ( 396-)  A      CB     0.61    2.29  INTRA BF
 731 SER   ( 232-)  B      N   <->  769 THR   ( 270-)  B      CG2    0.53    2.57  INTRA BL
1014 EDO   ( 809-)  A      C1  <-> 1052 HOH   ( 964 )  A      O      0.53    2.27  INTRA
 271 VAL   ( 273-)  A      CG1 <-> 1028 TAM   ( 823-)  A      C1     0.53    2.67  INTRA
 501 GLU   (   2-)  B      N   <->  502 THR   (   3-)  B      N      0.52    2.08  INTRA BF
 601 ARG   ( 102-)  B      NH1 <-> 1049 BOG   ( 800-)  B      C3     0.52    2.58  INTRA BF
 393 ARG   ( 395-)  A      CA  <->  394 ASP   ( 396-)  A      CB     0.50    2.50  INTRA BF
 903 ARG   ( 404-)  B      NH1 <-> 1005 TAM   ( 805-)  A      O4     0.48    2.22  INTRA BF
 731 SER   ( 232-)  B      O   <->  769 THR   ( 270-)  B      CG2    0.47    2.33  INTRA BL
 100 ARG   ( 102-)  A      NH1 <-> 1006 BOG   ( 701-)  A      O5     0.47    2.23  INTRA BF
 769 THR   ( 270-)  B      CG2 <->  770 THR   ( 271-)  B      N      0.46    2.54  INTRA BL
 894 ARG   ( 395-)  B      CG  <->  918 ARG   ( 419-)  B      NH2    0.44    2.66  INTRA BF
 896 ASP   ( 397-)  B      O   <->  900 ARG   ( 401-)  B      CD     0.43    2.37  INTRA BF
 890 ILE   ( 391-)  B      CG1 <->  891 GLU   ( 392-)  B      N      0.43    2.57  INTRA BF
 160 LYS   ( 162-)  A      O   <->  903 ARG   ( 404-)  B      CZ     0.39    2.41  INTRA
 313 GLY   ( 315-)  A      CA  <-> 1024 EDO   ( 818-)  A      C2     0.38    2.82  INTRA
 875 ILE   ( 376-)  B      CG1 <->  876 GLY   ( 377-)  B      N      0.37    2.63  INTRA
 393 ARG   ( 395-)  A      NH2 <->  413 ARG   ( 415-)  A      CD     0.36    2.74  INTRA BF
 417 ARG   ( 419-)  A      CG  <-> 1010 SO4   ( 803-)  A      O2     0.35    2.45  INTRA BF
And so on for a total of 182 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.

 995 ARG   ( 496-)  B      -6.82
 775 LYS   ( 276-)  B      -6.49
 612 LYS   ( 113-)  B      -6.42
 274 LYS   ( 276-)  A      -6.33
  56 HIS   (  58-)  A      -6.21
 494 ARG   ( 496-)  A      -6.12
 557 HIS   (  58-)  B      -6.12
 873 GLN   ( 374-)  B      -6.03
 998 LEU   ( 499-)  B      -6.03
 459 ARG   ( 461-)  A      -5.94
 960 ARG   ( 461-)  B      -5.94
 111 LYS   ( 113-)  A      -5.94
 372 GLN   ( 374-)  A      -5.83
 497 LEU   ( 499-)  A      -5.68
 623 ARG   ( 124-)  B      -5.50
 222 TYR   ( 224-)  A      -5.45
 403 ARG   ( 405-)  A      -5.42
 122 ARG   ( 124-)  A      -5.42
 956 HIS   ( 457-)  B      -5.40
 904 ARG   ( 405-)  B      -5.39
 492 GLN   ( 494-)  A      -5.36
 159 ARG   ( 161-)  A      -5.29
 455 HIS   ( 457-)  A      -5.27
 660 ARG   ( 161-)  B      -5.22
 390 GLU   ( 392-)  A      -5.19
 241 LYS   ( 243-)  A      -5.15
 993 GLN   ( 494-)  B      -5.15
 882 GLU   ( 383-)  B      -5.05
 381 GLU   ( 383-)  A      -5.04
 100 ARG   ( 102-)  A      -5.03
  92 HIS   (  94-)  A      -5.02

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.

 539 ALA   (  40-)  B   -3.08
  38 ALA   (  40-)  A   -3.06
 739 HIS   ( 240-)  B   -2.86
 238 HIS   ( 240-)  A   -2.85
  79 ILE   (  81-)  A   -2.63
 580 ILE   (  81-)  B   -2.63
 538 CYS   (  39-)  B   -2.60
  37 CYS   (  39-)  A   -2.59

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

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.

1052 HOH   (1067 )  A      O     59.88   38.34   40.15
1052 HOH   (1068 )  A      O     59.21   40.93   41.54

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.

1052 HOH   (1052 )  A      O
1052 HOH   (1056 )  A      O
1052 HOH   (1065 )  A      O
1053 HOH   (1053 )  B      O

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.

  12 ASN   (  14-)  A
  56 HIS   (  58-)  A
 126 ASN   ( 128-)  A
 177 ASN   ( 179-)  A
 248 ASN   ( 250-)  A
 288 ASN   ( 290-)  A
 295 ASN   ( 297-)  A
 340 ASN   ( 342-)  A
 422 ASN   ( 424-)  A
 442 HIS   ( 444-)  A
 476 ASN   ( 478-)  A
 480 GLN   ( 482-)  A
 590 HIS   (  91-)  B
 748 GLN   ( 249-)  B
 798 HIS   ( 299-)  B
 956 HIS   ( 457-)  B
 986 GLN   ( 487-)  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.

  12 ASN   (  14-)  A      N
  12 ASN   (  14-)  A      ND2
  32 ALA   (  34-)  A      N
  40 SER   (  42-)  A      N
  40 SER   (  42-)  A      OG
  44 SER   (  46-)  A      N
  46 LEU   (  48-)  A      N
  49 GLY   (  51-)  A      N
  55 GLU   (  57-)  A      N
  61 LEU   (  63-)  A      N
  84 ARG   (  86-)  A      NH1
  89 HIS   (  91-)  A      NE2
  96 ALA   (  98-)  A      N
  97 TRP   (  99-)  A      N
 122 ARG   ( 124-)  A      NE
 134 LYS   ( 136-)  A      N
 135 ARG   ( 137-)  A      N
 170 ALA   ( 172-)  A      N
 202 ASN   ( 204-)  A      ND2
 238 HIS   ( 240-)  A      N
 240 GLN   ( 242-)  A      NE2
 272 GLU   ( 274-)  A      N
 285 SER   ( 287-)  A      OG
 317 LEU   ( 319-)  A      N
 326 GLN   ( 328-)  A      N
And so on for a total of 73 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.

 288 ASN   ( 290-)  A      OD1
 392 ASP   ( 394-)  A      OD2
 785 GLU   ( 286-)  B      OE2
 893 ASP   ( 394-)  B      OD1

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.

1052 HOH   ( 839 )  A      O  1.02  K  4
1052 HOH   ( 865 )  A      O  1.03  K  4
1052 HOH   ( 883 )  A      O  0.93  K  4 H2O-B
1052 HOH   ( 891 )  A      O  0.96  K  4
1052 HOH   ( 942 )  A      O  1.10  K  4 H2O-B
1053 HOH   ( 837 )  B      O  0.99  K  4
1053 HOH   ( 845 )  B      O  1.10  K  4
1053 HOH   ( 924 )  B      O  1.10  K  4 Ion-B
1053 HOH   ( 958 )  B      O  1.08  K  4

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 107 ASP   ( 109-)  A   H-bonding suggests Asn
 390 GLU   ( 392-)  A   H-bonding suggests Gln
 392 ASP   ( 394-)  A   H-bonding suggests Asn; Ligand-contact

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 :  -0.718
  2nd generation packing quality :  -1.801
  Ramachandran plot appearance   :  -1.102
  chi-1/chi-2 rotamer normality  :  -2.066
  Backbone conformation          :  -0.706

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.516 (tight)
  Bond angles                    :   0.788
  Omega angle restraints         :   1.500 (loose)
  Side chain planarity           :   2.125 (loose)
  Improper dihedral distribution :   1.711 (loose)
  B-factor distribution          :   0.830
  Inside/Outside distribution    :   1.004

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.75


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -2.1
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :  -1.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.516 (tight)
  Bond angles                    :   0.788
  Omega angle restraints         :   1.500 (loose)
  Side chain planarity           :   2.125 (loose)
  Improper dihedral distribution :   1.711 (loose)
  B-factor distribution          :   0.830
  Inside/Outside distribution    :   1.004
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.