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 pdb2qpe.ent

Checks that need to be done early-on in validation

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.

 761 HAS   ( 801-)  A  -         Atom types
 762 CUA   ( 802-)  B  -         Atom types
 763 HEM   ( 800-)  A  -         OK

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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.

   1 SER   (   6-)  A    High
   2 GLU   (   7-)  A    High
   3 ILE   (   8-)  A    High
   4 SER   (   9-)  A    High
   5 ARG   (  10-)  A    High
   6 VAL   (  11-)  A    High
   7 TYR   (  12-)  A    High
   8 GLU   (  13-)  A    High
   9 ALA   (  14-)  A    High
  10 TYR   (  15-)  A    High
  11 PRO   (  16-)  A    High
  12 GLU   (  17-)  A    High
  14 LYS   (  19-)  A    High
  17 LEU   (  22-)  A    High
  18 TYR   (  23-)  A    High
  21 VAL   (  26-)  A    High
  22 LEU   (  27-)  A    High
  24 PHE   (  29-)  A    High
  25 LEU   (  30-)  A    High
  32 LEU   (  37-)  A    High
  45 ASP   (  50-)  A    High
  47 TYR   (  52-)  A    High
  49 LEU   (  54-)  A    High
  50 LEU   (  55-)  A    High
  51 LYS   (  56-)  A    High
And so on for a total of 272 lines.

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: 1

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

   5 ARG   (  10-)  A
  52 ARG   (  57-)  A
  90 ARG   (  95-)  A
  95 ARG   ( 100-)  A
 163 ARG   ( 168-)  A
 164 ARG   ( 169-)  A
 220 ARG   ( 225-)  A
 320 ARG   ( 325-)  A
 322 ARG   ( 327-)  A
 325 ARG   ( 330-)  A
 413 ARG   ( 418-)  A
 444 ARG   ( 449-)  A
 445 ARG   ( 450-)  A
 490 ARG   ( 495-)  A
 513 ARG   ( 518-)  A
 521 ARG   ( 526-)  A
 555 ARG   ( 560-)  A
 607 ARG   (  52-)  B
 614 ARG   (  59-)  B
 691 ARG   ( 136-)  B
 696 ARG   ( 141-)  B
 701 ARG   ( 146-)  B
 755 ARG   (  33-)  C

Warning: Tyrosine convention problem

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

  18 TYR   (  23-)  A
  60 TYR   (  65-)  A
  61 TYR   (  66-)  A
 131 TYR   ( 136-)  A
 156 TYR   ( 161-)  A
 239 TYR   ( 244-)  A
 243 TYR   ( 248-)  A
 368 TYR   ( 373-)  A
 447 TYR   ( 452-)  A
 481 TYR   ( 486-)  A
 569 TYR   (  14-)  B
 634 TYR   (  79-)  B
 692 TYR   ( 137-)  B

Warning: Phenylalanine convention problem

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

  19 PHE   (  24-)  A
  24 PHE   (  29-)  A
  33 PHE   (  38-)  A
  36 PHE   (  41-)  A
 109 PHE   ( 114-)  A
 147 PHE   ( 152-)  A
 189 PHE   ( 194-)  A
 208 PHE   ( 213-)  A
 267 PHE   ( 272-)  A
 276 PHE   ( 281-)  A
 280 PHE   ( 285-)  A
 299 PHE   ( 304-)  A
 317 PHE   ( 322-)  A
 364 PHE   ( 369-)  A
 424 PHE   ( 429-)  A
 484 PHE   ( 489-)  A
 526 PHE   ( 531-)  A
 576 PHE   (  21-)  B
 582 PHE   (  27-)  B
 584 PHE   (  29-)  B
 643 PHE   (  88-)  B
 694 PHE   ( 139-)  B
 716 PHE   ( 161-)  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.

  45 ASP   (  50-)  A
 160 ASP   ( 165-)  A
 282 ASP   ( 287-)  A
 286 ASP   ( 291-)  A
 367 ASP   ( 372-)  A
 410 ASP   ( 415-)  A
 512 ASP   ( 517-)  A
 520 ASP   ( 525-)  A

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.

  91 GLU   (  96-)  A
 123 GLU   ( 128-)  A
 198 GLU   ( 203-)  A
 212 GLU   ( 217-)  A
 316 GLU   ( 321-)  A
 495 GLU   ( 500-)  A
 498 GLU   ( 503-)  A
 606 GLU   (  51-)  B
 657 GLU   ( 102-)  B
 674 GLU   ( 119-)  B
 699 GLU   ( 144-)  B
 725 GLU   (   3-)  C

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  85 VAL   (  90-)  A      CA   CB    1.62    4.5
 114 VAL   ( 119-)  A      CA   CB    1.63    5.2
 542 VAL   ( 547-)  A      CA   CB    1.63    4.8
 571 LYS   (  16-)  B      CE   NZ    1.62    4.4
 627 VAL   (  72-)  B      CA   CB    1.64    5.4

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

 |  0.996473 -0.000497  0.000436|
 | -0.000497  0.997981 -0.000315|
 |  0.000436 -0.000315  0.996584|
Proposed new scale matrix

 |  0.008754  0.000004 -0.000004|
 |  0.000004  0.008741  0.000003|
 | -0.000003  0.000002  0.006754|
With corresponding cell

    A    = 114.235  B   = 114.408  C    = 148.059
    Alpha=  90.036  Beta=  89.950  Gamma=  90.057

The CRYST1 cell dimensions

    A    = 114.635  B   = 114.635  C    = 148.568
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 232.943
(Under-)estimated Z-score: 11.248

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.

  20 LEU   (  25-)  A      CB   CG   CD1  93.71   -5.7
 133 PRO   ( 138-)  A      N    CA   C   121.83    4.0
 213 GLY   ( 218-)  A      N    CA   C   126.12    4.7
 218 VAL   ( 223-)  A      N    CA   CB  117.40    4.1
 225 TRP   ( 230-)  A      CA   CB   CG  121.52    4.2
 233 PHE   ( 238-)  A      C    CA   CB  117.82    4.1
 285 ILE   ( 290-)  A      C    CA   CB  118.65    4.5
 300 VAL   ( 305-)  A     -C    N    CA  113.00   -4.8
 304 SER   ( 309-)  A      CA   CB   OG  101.18   -5.0
 306 MET   ( 311-)  A      CB   CG   SD   99.32   -4.5
 379 HIS   ( 384-)  A      CG   ND1  CE1 109.93    4.3
 547 HIS   ( 552-)  A      CG   ND1  CE1 109.70    4.1
 643 PHE   (  88-)  B     -C    N    CA  130.33    4.8
 643 PHE   (  88-)  B      C    CA   CB  118.54    4.4
 650 ILE   (  95-)  B      N    CA   C    99.79   -4.1
 668 ILE   ( 113-)  B      C    CA   CB  101.91   -4.3
 701 ARG   ( 146-)  B      CB   CG   CD  106.08   -4.0
 701 ARG   ( 146-)  B      CG   CD   NE  117.61    4.2
 710 LEU   ( 155-)  B      N    CA   C   122.73    4.1
 721 VAL   ( 166-)  B      N    CA   CB  117.32    4.0
 755 ARG   (  33-)  C      CB   CG   CD  105.81   -4.1
 755 ARG   (  33-)  C      CG   CD   NE  120.27    5.7

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.

   5 ARG   (  10-)  A
  45 ASP   (  50-)  A
  52 ARG   (  57-)  A
  90 ARG   (  95-)  A
  91 GLU   (  96-)  A
  95 ARG   ( 100-)  A
 123 GLU   ( 128-)  A
 160 ASP   ( 165-)  A
 163 ARG   ( 168-)  A
 164 ARG   ( 169-)  A
 198 GLU   ( 203-)  A
 212 GLU   ( 217-)  A
 220 ARG   ( 225-)  A
 282 ASP   ( 287-)  A
 286 ASP   ( 291-)  A
 316 GLU   ( 321-)  A
 320 ARG   ( 325-)  A
 322 ARG   ( 327-)  A
 325 ARG   ( 330-)  A
 367 ASP   ( 372-)  A
 410 ASP   ( 415-)  A
 413 ARG   ( 418-)  A
 444 ARG   ( 449-)  A
 445 ARG   ( 450-)  A
 490 ARG   ( 495-)  A
 495 GLU   ( 500-)  A
 498 GLU   ( 503-)  A
 512 ASP   ( 517-)  A
 513 ARG   ( 518-)  A
 520 ASP   ( 525-)  A
 521 ARG   ( 526-)  A
 555 ARG   ( 560-)  A
 606 GLU   (  51-)  B
 607 ARG   (  52-)  B
 614 ARG   (  59-)  B
 657 GLU   ( 102-)  B
 674 GLU   ( 119-)  B
 691 ARG   ( 136-)  B
 696 ARG   ( 141-)  B
 699 GLU   ( 144-)  B
 701 ARG   ( 146-)  B
 725 GLU   (   3-)  C
 755 ARG   (  33-)  C

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.

 643 PHE   (  88-)  B      CA    -7.8    21.45    33.98
The average deviation= 1.349

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.

 213 GLY   ( 218-)  A    6.41
  98 MET   ( 103-)  A    6.08
 257 ASP   ( 262-)  A    5.14
 460 VAL   ( 465-)  A    5.11
 710 LEU   ( 155-)  B    4.65
 343 ALA   ( 348-)  A    4.62
 185 TRP   ( 190-)  A    4.62
 437 ALA   ( 442-)  A    4.54
 579 ALA   (  24-)  B    4.49
 266 LEU   ( 271-)  A    4.18
 355 GLY   ( 360-)  A    4.12
  50 LEU   (  55-)  A    4.11
  61 TYR   (  66-)  A    4.02
 225 TRP   ( 230-)  A    4.02

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 : 1.685

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.

 228 HIS   ( 233-)  A    4.33

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.402

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.

 364 PHE   ( 369-)  A    -3.3
 174 THR   ( 179-)  A    -3.0
 749 TYR   (  27-)  C    -2.9
 335 PRO   ( 340-)  A    -2.8
 649 PRO   (  94-)  B    -2.7
 629 THR   (  74-)  B    -2.7
 104 SER   ( 109-)  A    -2.7
 325 ARG   ( 330-)  A    -2.7
 205 PRO   ( 210-)  A    -2.7
 456 PRO   ( 461-)  A    -2.6
 321 LEU   ( 326-)  A    -2.6
 542 VAL   ( 547-)  A    -2.5
 743 VAL   (  21-)  C    -2.5
 663 THR   ( 108-)  B    -2.5
 585 ILE   (  30-)  B    -2.5
 407 PRO   ( 412-)  A    -2.5
 211 VAL   ( 216-)  A    -2.4
 256 SER   ( 261-)  A    -2.4
 594 THR   (  39-)  B    -2.4
 627 VAL   (  72-)  B    -2.4
  23 GLY   (  28-)  A    -2.4
 697 PRO   ( 142-)  B    -2.4
 171 GLY   ( 176-)  A    -2.3
 389 THR   ( 394-)  A    -2.3
 416 GLY   ( 421-)  A    -2.3
And so on for a total of 64 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.

   3 ILE   (   8-)  A  omega poor
   6 VAL   (  11-)  A  Poor phi/psi, omega poor
   7 TYR   (  12-)  A  omega poor
  12 GLU   (  17-)  A  omega poor
  23 GLY   (  28-)  A  Poor phi/psi
  43 ASN   (  48-)  A  Poor phi/psi
  47 TYR   (  52-)  A  PRO omega poor
  52 ARG   (  57-)  A  Poor phi/psi, omega poor
  53 LEU   (  58-)  A  Poor phi/psi
  59 SER   (  64-)  A  omega poor
  63 GLY   (  68-)  A  Poor phi/psi
  84 MET   (  89-)  A  Poor phi/psi, omega poor
  97 ASN   ( 102-)  A  Poor phi/psi
  98 MET   ( 103-)  A  omega poor
 103 LEU   ( 108-)  A  omega poor
 104 SER   ( 109-)  A  Poor phi/psi
 108 ALA   ( 113-)  A  omega poor
 109 PHE   ( 114-)  A  omega poor
 111 GLY   ( 116-)  A  Poor phi/psi
 113 VAL   ( 118-)  A  omega poor
 122 ASN   ( 127-)  A  Poor phi/psi
 127 LEU   ( 132-)  A  Poor phi/psi
 132 PRO   ( 137-)  A  PRO omega poor
 134 LEU   ( 139-)  A  omega poor
 139 ALA   ( 144-)  A  omega poor
And so on for a total of 110 lines.

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 : -5.551

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.

 577 SER   (  22-)  B    0.40

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!

   3 ILE   (   8-)  A      0
   4 SER   (   9-)  A      0
   5 ARG   (  10-)  A      0
   6 VAL   (  11-)  A      0
   8 GLU   (  13-)  A      0
  43 ASN   (  48-)  A      0
  46 ALA   (  51-)  A      0
  54 LEU   (  59-)  A      0
  56 PHE   (  61-)  A      0
  73 ILE   (  78-)  A      0
  84 MET   (  89-)  A      0
  94 MET   (  99-)  A      0
  97 ASN   ( 102-)  A      0
  98 MET   ( 103-)  A      0
 122 ASN   ( 127-)  A      0
 124 ALA   ( 129-)  A      0
 125 THR   ( 130-)  A      0
 126 VAL   ( 131-)  A      0
 127 LEU   ( 132-)  A      0
 131 TYR   ( 136-)  A      0
 132 PRO   ( 137-)  A      0
 133 PRO   ( 138-)  A      0
 134 LEU   ( 139-)  A      0
 135 LYS   ( 140-)  A      0
 137 HIS   ( 142-)  A      0
And so on for a total of 210 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 : 8.639

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!

 171 GLY   ( 176-)  A   1.78   80

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]

 118 PRO   ( 123-)  A    0.18 LOW
 353 PRO   ( 358-)  A    0.10 LOW
 461 PRO   ( 466-)  A    0.20 LOW
 601 PRO   (  46-)  B    0.48 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].

  48 PRO   (  53-)  A   104.7 envelop C-beta (108 degrees)
  88 PRO   (  93-)  A  -121.4 half-chair C-delta/C-gamma (-126 degrees)
 133 PRO   ( 138-)  A    49.3 half-chair C-delta/C-gamma (54 degrees)
 205 PRO   ( 210-)  A   159.5 half-chair C-alpha/N (162 degrees)
 216 PRO   ( 221-)  A     8.5 envelop N (0 degrees)
 229 PRO   ( 234-)  A   177.3 envelop N (180 degrees)
 258 PRO   ( 263-)  A  -117.1 half-chair C-delta/C-gamma (-126 degrees)
 283 PRO   ( 288-)  A   -46.8 half-chair C-beta/C-alpha (-54 degrees)
 287 PRO   ( 292-)  A  -153.3 half-chair N/C-delta (-162 degrees)
 303 PRO   ( 308-)  A  -157.7 half-chair N/C-delta (-162 degrees)
 335 PRO   ( 340-)  A    -6.5 envelop N (0 degrees)
 407 PRO   ( 412-)  A    -8.8 envelop N (0 degrees)
 456 PRO   ( 461-)  A   154.1 half-chair C-alpha/N (162 degrees)
 500 PRO   ( 505-)  A     2.1 envelop N (0 degrees)
 539 PRO   ( 544-)  A    42.1 envelop C-delta (36 degrees)
 622 PRO   (  67-)  B   -30.2 envelop C-alpha (-36 degrees)
 647 PRO   (  92-)  B    48.9 half-chair C-delta/C-gamma (54 degrees)
 649 PRO   (  94-)  B    29.4 envelop C-delta (36 degrees)
 653 PRO   (  98-)  B    47.0 half-chair C-delta/C-gamma (54 degrees)
 697 PRO   ( 142-)  B   -62.1 half-chair C-beta/C-alpha (-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.

 228 HIS   ( 233-)  A      NE2 <->  232 TYR   ( 237-)  A      CE2    1.39    1.71  INTRA BL
 380 PHE   ( 385-)  A      CB  <->  761 HAS   ( 801-)  A      CMA    0.67    2.53  INTRA BL
 228 HIS   ( 233-)  A      ND1 <->  277 HIS   ( 282-)  A      CE1    0.63    2.47  INTRA BL
  40 ASN   (  45-)  A      ND2 <->   60 TYR   (  65-)  A      CE2    0.63    2.47  INTRA BL
 405 GLY   ( 410-)  A      CA  <->  497 ALA   ( 502-)  A      CB     0.60    2.60  INTRA BF
 380 PHE   ( 385-)  A      CG  <->  761 HAS   ( 801-)  A      CMA    0.59    2.61  INTRA BL
 228 HIS   ( 233-)  A      CD2 <->  232 TYR   ( 237-)  A      CE2    0.59    2.61  INTRA BL
   5 ARG   (  10-)  A      O   <->    7 TYR   (  12-)  A      N      0.48    2.22  INTRA BF
 272 THR   ( 277-)  A      N   <->  273 PRO   ( 278-)  A      CD     0.45    2.55  INTRA BL
 228 HIS   ( 233-)  A      NE2 <->  232 TYR   ( 237-)  A      CD2    0.45    2.65  INTRA BF
 215 ASP   ( 220-)  A      OD2 <->  607 ARG   (  52-)  B      NH2    0.44    2.26  INTRA BF
 316 GLU   ( 321-)  A      OE2 <->  320 ARG   ( 325-)  A      NH1    0.44    2.26  INTRA BF
  58 GLN   (  63-)  A      CG  <->  122 ASN   ( 127-)  A      ND2    0.43    2.67  INTRA BF
 641 PHE   (  86-)  B      O   <->  643 PHE   (  88-)  B      N      0.42    2.28  INTRA BL
 277 HIS   ( 282-)  A      CD2 <->  278 HIS   ( 283-)  A      CD2    0.42    2.78  INTRA BL
 228 HIS   ( 233-)  A      CE1 <->  232 TYR   ( 237-)  A      CE2    0.42    2.78  INTRA BF
 381 HIS   ( 386-)  A      NE2 <->  763 HEM   ( 800-)  A      NA     0.41    2.59  INTRA BL
   9 ALA   (  14-)  A      O   <->   95 ARG   ( 100-)  A      NH2    0.41    2.29  INTRA BF
 277 HIS   ( 282-)  A      NE2 <->  278 HIS   ( 283-)  A      CD2    0.40    2.70  INTRA BL
 228 HIS   ( 233-)  A      CE1 <->  277 HIS   ( 282-)  A      CE1    0.40    2.80  INTRA BF
 546 GLY   ( 551-)  A      C   <->  547 HIS   ( 552-)  A      ND1    0.39    2.61  INTRA BF
 228 HIS   ( 233-)  A      ND1 <->  277 HIS   ( 282-)  A      NE2    0.38    2.62  INTRA BL
 454 ALA   ( 459-)  A      C   <->  456 PRO   ( 461-)  A      CD     0.36    2.84  INTRA BL
 454 ALA   ( 459-)  A      O   <->  701 ARG   ( 146-)  B      NH2    0.36    2.34  INTRA BL
  67 HIS   (  72-)  A      NE2 <->  763 HEM   ( 800-)  A      NC     0.35    2.65  INTRA BL
And so on for a total of 302 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 325 ARG   ( 330-)  A      -7.25
 696 ARG   ( 141-)  B      -7.09
 322 ARG   ( 327-)  A      -6.31
 492 ARG   ( 497-)  A      -6.07
 210 LEU   ( 215-)  A      -5.85
 490 ARG   ( 495-)  A      -5.77
 607 ARG   (  52-)  B      -5.61
 595 HIS   (  40-)  B      -5.58
 450 GLN   ( 455-)  A      -5.57
 444 ARG   ( 449-)  A      -5.55
 695 LYS   ( 140-)  B      -5.53
 555 ARG   ( 560-)  A      -5.51
 249 GLN   ( 254-)  A      -5.36
   3 ILE   (   8-)  A      -5.36
 128 TYR   ( 133-)  A      -5.23
 278 HIS   ( 283-)  A      -5.14
 131 TYR   ( 136-)  A      -5.06
 714 ASN   ( 159-)  B      -5.05
 614 ARG   (  59-)  B      -5.03
 212 GLU   ( 217-)  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.

   1 SER   (   6-)  A         3 - ILE      8- ( A)         -4.56
 614 ARG   (  59-)  B       616 - GLU     61- ( B)         -4.64

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

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.

 620 ALA   (  65-)  B   -2.98
   9 ALA   (  14-)  A   -2.76
  92 LEU   (  97-)  A   -2.71
 454 ALA   ( 459-)  A   -2.58

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 563 HIS   (   8-)  B
 672 HIS   ( 117-)  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.

   3 ILE   (   8-)  A      N
   4 SER   (   9-)  A      N
   5 ARG   (  10-)  A      N
   6 VAL   (  11-)  A      N
   7 TYR   (  12-)  A      N
  37 GLN   (  42-)  A      NE2
  43 ASN   (  48-)  A      ND2
  47 TYR   (  52-)  A      OH
  56 PHE   (  61-)  A      N
  59 SER   (  64-)  A      N
  60 TYR   (  65-)  A      OH
  61 TYR   (  66-)  A      N
  71 ASN   (  76-)  A      ND2
  90 ARG   (  95-)  A      NH1
  95 ARG   ( 100-)  A      NE
  97 ASN   ( 102-)  A      N
 105 TRP   ( 110-)  A      NE1
 124 ALA   ( 129-)  A      N
 128 TYR   ( 133-)  A      N
 129 THR   ( 134-)  A      N
 131 TYR   ( 136-)  A      N
 141 TYR   ( 146-)  A      OH
 211 VAL   ( 216-)  A      N
 220 ARG   ( 225-)  A      NE
 232 TYR   ( 237-)  A      OH
And so on for a total of 98 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.

  37 GLN   (  42-)  A      OE1
  71 ASN   (  76-)  A      OD1
 198 GLU   ( 203-)  A      OE1
 279 GLN   ( 284-)  A      OE1
 367 ASP   ( 372-)  A      OD1
 383 GLN   ( 388-)  A      OE1
 435 HIS   ( 440-)  A      NE2
 465 ASN   ( 470-)  A      OD1
 498 GLU   ( 503-)  A      OE1
 498 GLU   ( 503-)  A      OE2
 570 GLU   (  15-)  B      OE1
 672 HIS   ( 117-)  B      NE2

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.

  91 GLU   (  96-)  A   H-bonding suggests Gln
 198 GLU   ( 203-)  A   H-bonding suggests Gln
 316 GLU   ( 321-)  A   H-bonding suggests Gln
 337 ASP   ( 342-)  A   H-bonding suggests Asn; but Alt-Rotamer
 570 GLU   (  15-)  B   H-bonding suggests Gln; but Alt-Rotamer

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 :  -1.335
  2nd generation packing quality :  -1.623
  Ramachandran plot appearance   :  -5.402 (bad)
  chi-1/chi-2 rotamer normality  :  -5.551 (bad)
  Backbone conformation          :  -0.439

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.886
  Bond angles                    :   1.049
  Omega angle restraints         :   1.571 (loose)
  Side chain planarity           :   0.778
  Improper dihedral distribution :   1.184
  B-factor distribution          :   1.036
  Inside/Outside distribution    :   1.154

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -2.8
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.886
  Bond angles                    :   1.049
  Omega angle restraints         :   1.571 (loose)
  Side chain planarity           :   0.778
  Improper dihedral distribution :   1.184
  B-factor distribution          :   1.036
  Inside/Outside distribution    :   1.154
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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      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.