WHAT IF Check report

This file was created 2014-10-03 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 pdb3r5x.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1
Number of matrices in space group: 1
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 2 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

1185 ATP   ( 311-)  A  -
1187 ATP   ( 311-)  B  -
1190 ATP   ( 311-)  C  -
1196 ACY   ( 314-)  D  -
1197 ATP   ( 311-)  D  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 495 ARG   ( 196-)  B  -
 692 SER   (  98-)  C  -
 766 GLU   ( 178-)  C  -
 832 MSE   ( 259-)  C  -
 849 SER   ( 276-)  C  -
 898 MSE   (  19-)  D  -
 931 ASP   (  52-)  D  -
1037 MSE   ( 158-)  D  -
1082 ASP   ( 203-)  D  -
1088 ASP   ( 209-)  D  -
1129 MSE   ( 250-)  D  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 495 ARG   ( 196-)  B  -
 692 SER   (  98-)  C  -
 766 GLU   ( 178-)  C  -
 832 MSE   ( 259-)  C  -
 849 SER   ( 276-)  C  -
 898 MSE   (  19-)  D  -
 931 ASP   (  52-)  D  -
1037 MSE   ( 158-)  D  -
1082 ASP   ( 203-)  D  -
1088 ASP   ( 209-)  D  -
1129 MSE   ( 250-)  D  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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   (  -2-)  A    High
   2 ASN   (  -1-)  A    High
   4 MSE   ( 313-)  A    High
  44 ASN   (  41-)  A    High
  45 GLU   (  42-)  A    High
  51 GLU   (  48-)  A    High
  54 LYS   (  51-)  A    High
  55 ASP   (  52-)  A    High
 121 MSE   ( 118-)  A    High
 123 ASP   ( 120-)  A    High
 128 GLU   ( 125-)  A    High
 130 ASP   ( 127-)  A    High
 142 SER   ( 143-)  A    High
 143 VAL   ( 144-)  A    High
 144 GLY   ( 145-)  A    High
 146 LYS   ( 147-)  A    High
 157 MSE   ( 158-)  A    High
 159 GLU   ( 160-)  A    High
 163 GLU   ( 164-)  A    High
 164 TRP   ( 165-)  A    High
 187 LYS   ( 188-)  A    High
 225 GLU   ( 226-)  A    High
 302 GLY   ( 303-)  A    High
 315 SER   (  12-)  B    High
 333 LYS   (  30-)  B    High
And so on for a total of 150 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   4 MSE   ( 313-)  A    0.59
  10 MSE   (   7-)  A    0.68
  22 MSE   (  19-)  A    0.35
  27 MSE   (  24-)  A    0.66
  47 MSE   (  44-)  A    0.43
  89 MSE   (  86-)  A    0.67
  96 MSE   (  93-)  A    0.66
 157 MSE   ( 158-)  A    0.70
 248 MSE   ( 249-)  A    0.73
 249 MSE   ( 250-)  A    0.48
 258 MSE   ( 259-)  A    0.85
 266 MSE   ( 267-)  A    0.62
 289 MSE   ( 290-)  A    0.58
 304 MSE   (   1-)  B    0.54
 310 MSE   (   7-)  B    0.67
 322 MSE   (  19-)  B    0.57
 327 MSE   (  24-)  B    0.63
 347 MSE   (  44-)  B    0.40
 389 MSE   (  86-)  B    0.69
 396 MSE   (  93-)  B    0.59
 457 MSE   ( 158-)  B    0.51
 539 MSE   ( 249-)  B    0.67
 540 MSE   ( 250-)  B    0.61
 557 MSE   ( 267-)  B    0.64
 580 MSE   ( 290-)  B    0.53
 595 MSE   (   1-)  C    0.57
 601 MSE   (   7-)  C    0.72
 613 MSE   (  19-)  C    0.56
 618 MSE   (  24-)  C    0.64
 638 MSE   (  44-)  C    0.30
 680 MSE   (  86-)  C    0.82
 687 MSE   (  93-)  C    0.69
 746 MSE   ( 158-)  C    0.53
 822 MSE   ( 249-)  C    0.77
 823 MSE   ( 250-)  C    0.50
 840 MSE   ( 267-)  C    0.66
 863 MSE   ( 290-)  C    0.54
 880 MSE   (   1-)  D    0.52
 886 MSE   (   7-)  D    0.65
 903 MSE   (  24-)  D    0.71
 923 MSE   (  44-)  D    0.43
 965 MSE   (  86-)  D    0.88
 972 MSE   (  93-)  D    0.69
 997 MSE   ( 118-)  D    0.56
1138 MSE   ( 259-)  D    0.59
1146 MSE   ( 267-)  D    0.68
1169 MSE   ( 290-)  D    0.49

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: 4

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 195 ARG   ( 196-)  A
 226 ARG   ( 227-)  A
 245 ARG   ( 246-)  A
 536 ARG   ( 246-)  B
 819 ARG   ( 246-)  C
1125 ARG   ( 246-)  D

Warning: Tyrosine convention problem

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

  67 TYR   (  64-)  A
 149 TYR   ( 150-)  A
 207 TYR   ( 208-)  A
 243 TYR   ( 244-)  A
 449 TYR   ( 150-)  B
 547 TYR   ( 257-)  B
 658 TYR   (  64-)  C
 675 TYR   (  81-)  C
 738 TYR   ( 150-)  C
 809 TYR   ( 236-)  C
 817 TYR   ( 244-)  C
 943 TYR   (  64-)  D
1083 TYR   ( 204-)  D
1115 TYR   ( 236-)  D
1123 TYR   ( 244-)  D

Warning: Phenylalanine convention problem

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

  58 PHE   (  55-)  A
 126 PHE   ( 123-)  A
 184 PHE   ( 185-)  A
 201 PHE   ( 202-)  A
 484 PHE   ( 185-)  B
 649 PHE   (  55-)  C
 717 PHE   ( 123-)  C
 877 PHE   ( 304-)  C
 934 PHE   (  55-)  D
1064 PHE   ( 185-)  D
1183 PHE   ( 304-)  D

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  97 ASP   (  94-)  A
 208 ASP   ( 209-)  A
 209 ASP   ( 210-)  A
 397 ASP   (  94-)  B
 688 ASP   (  94-)  C
 718 ASP   ( 124-)  C
 721 ASP   ( 127-)  C
 739 ASP   ( 151-)  C
 741 ASP   ( 153-)  C
 754 ASP   ( 166-)  C
 973 ASP   (  94-)  D
1032 ASP   ( 153-)  D

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  45 GLU   (  42-)  A
 153 GLU   ( 154-)  A
 163 GLU   ( 164-)  A
 199 GLU   ( 200-)  A
 215 GLU   ( 216-)  A
 316 GLU   (  13-)  B
 378 GLU   (  75-)  B
 459 GLU   ( 160-)  B
 506 GLU   ( 216-)  B
 516 GLU   ( 226-)  B
 636 GLU   (  42-)  C
 702 GLU   ( 108-)  C
 713 GLU   ( 119-)  C
 748 GLU   ( 160-)  C
 756 GLU   ( 168-)  C
 796 GLU   ( 223-)  C
 799 GLU   ( 226-)  C
 913 GLU   (  34-)  D
1033 GLU   ( 154-)  D

Error: Decreasing residue numbers

At least one residue in each of the chains mentioned below has a residue number that is lower than the previous residue in that chain ('-' represents a chain without chain identifier).

Chain identifier(s): A

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.999053  0.000219  0.000675|
 |  0.000219  0.998468 -0.001233|
 |  0.000675 -0.001233  0.998986|
Proposed new scale matrix

 |  0.017769 -0.004614 -0.000334|
 |  0.000000  0.014992 -0.004254|
 | -0.000008  0.000014  0.011310|
With corresponding cell

    A    =  56.281  B   =  68.895  C    =  92.240
    Alpha=  73.474  Beta=  84.876  Gamma=  75.433

The CRYST1 cell dimensions

    A    =  56.336  B   =  68.992  C    =  92.387
    Alpha=  73.360  Beta=  84.960  Gamma=  75.460

Variance: 68.557
(Under-)estimated Z-score: 6.102

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.

 856 HIS   ( 283-)  C      CG   ND1  CE1 109.64    4.0
1077 ALA   ( 198-)  D     -C    N    CA  113.50   -4.6
1162 HIS   ( 283-)  D      CG   ND1  CE1 109.83    4.2

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.

  45 GLU   (  42-)  A
  97 ASP   (  94-)  A
 153 GLU   ( 154-)  A
 163 GLU   ( 164-)  A
 195 ARG   ( 196-)  A
 199 GLU   ( 200-)  A
 208 ASP   ( 209-)  A
 209 ASP   ( 210-)  A
 215 GLU   ( 216-)  A
 226 ARG   ( 227-)  A
 245 ARG   ( 246-)  A
 316 GLU   (  13-)  B
 378 GLU   (  75-)  B
 397 ASP   (  94-)  B
 459 GLU   ( 160-)  B
 506 GLU   ( 216-)  B
 516 GLU   ( 226-)  B
 536 ARG   ( 246-)  B
 636 GLU   (  42-)  C
 688 ASP   (  94-)  C
 702 GLU   ( 108-)  C
 713 GLU   ( 119-)  C
 718 ASP   ( 124-)  C
 721 ASP   ( 127-)  C
 739 ASP   ( 151-)  C
 741 ASP   ( 153-)  C
 748 GLU   ( 160-)  C
 754 ASP   ( 166-)  C
 756 GLU   ( 168-)  C
 796 GLU   ( 223-)  C
 799 GLU   ( 226-)  C
 819 ARG   ( 246-)  C
 913 GLU   (  34-)  D
 973 ASP   (  94-)  D
1032 ASP   ( 153-)  D
1033 GLU   ( 154-)  D
1125 ARG   ( 246-)  D

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.

1077 ALA   ( 198-)  D      C      6.1     9.44     0.08
The average deviation= 0.886

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.

  69 GLU   (  66-)  A    5.83
 906 ASN   (  27-)  D    5.22
  30 ASN   (  27-)  A    4.32
 945 GLU   (  66-)  D    4.19

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.

 314 SER   (  11-)  B    -2.6
1143 LEU   ( 264-)  D    -2.4
 784 ARG   ( 196-)  C    -2.4
 447 ILE   ( 148-)  B    -2.3
 263 LEU   ( 264-)  A    -2.3
 837 LEU   ( 264-)  C    -2.3
 554 LEU   ( 264-)  B    -2.3
 816 VAL   ( 243-)  C    -2.2
 195 ARG   ( 196-)  A    -2.2
 217 ILE   ( 218-)  A    -2.1
 202 ASP   ( 203-)  A    -2.1
 636 GLU   (  42-)  C    -2.1
 533 VAL   ( 243-)  B    -2.1
 454 LEU   ( 155-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  14 SER   (  11-)  A  Poor phi/psi
  36 TYR   (  33-)  A  omega poor
  44 ASN   (  41-)  A  omega poor
 119 THR   ( 116-)  A  omega poor
 134 PHE   ( 131-)  A  PRO omega poor
 198 ALA   ( 199-)  A  omega poor
 201 PHE   ( 202-)  A  omega poor
 202 ASP   ( 203-)  A  Poor phi/psi
 239 LYS   ( 240-)  A  Poor phi/psi
 242 VAL   ( 243-)  A  Poor phi/psi
 265 GLY   ( 266-)  A  Poor phi/psi
 314 SER   (  11-)  B  Poor phi/psi
 335 LYS   (  32-)  B  omega poor
 336 TYR   (  33-)  B  omega poor
 434 PHE   ( 131-)  B  PRO omega poor
 530 LYS   ( 240-)  B  Poor phi/psi
 533 VAL   ( 243-)  B  Poor phi/psi
 550 GLU   ( 260-)  B  Poor phi/psi
 605 SER   (  11-)  C  Poor phi/psi
 626 LYS   (  32-)  C  omega poor
 635 ASN   (  41-)  C  omega poor
 725 PHE   ( 131-)  C  PRO omega poor
 753 TRP   ( 165-)  C  omega poor
 813 LYS   ( 240-)  C  Poor phi/psi
 816 VAL   ( 243-)  C  Poor phi/psi
 890 SER   (  11-)  D  Poor phi/psi
 912 TYR   (  33-)  D  omega poor
 919 LEU   (  40-)  D  omega poor
1010 PHE   ( 131-)  D  PRO omega poor
1088 ASP   ( 209-)  D  omega poor
1119 LYS   ( 240-)  D  Poor phi/psi
1122 VAL   ( 243-)  D  Poor phi/psi
1139 GLU   ( 260-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.213

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.

 858 SER   ( 285-)  C    0.35
 683 SER   (  89-)  C    0.35
1036 SER   ( 157-)  D    0.35
 968 SER   (  89-)  D    0.35
 156 SER   ( 157-)  A    0.36
  92 SER   (  89-)  A    0.36
  91 SER   (  88-)  A    0.37
 575 SER   ( 285-)  B    0.37
 977 SER   (  98-)  D    0.38
 284 SER   ( 285-)  A    0.38
 611 SER   (  17-)  C    0.39
 682 SER   (  88-)  C    0.39
 275 SER   ( 276-)  A    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!

   4 MSE   ( 313-)  A      0
  10 MSE   (   7-)  A      0
  13 VAL   (  10-)  A      0
  14 SER   (  11-)  A      0
  22 MSE   (  19-)  A      0
  27 MSE   (  24-)  A      0
  35 LYS   (  32-)  A      0
  44 ASN   (  41-)  A      0
  45 GLU   (  42-)  A      0
  47 MSE   (  44-)  A      0
  53 ALA   (  50-)  A      0
  62 ALA   (  59-)  A      0
  64 HIS   (  61-)  A      0
  66 LYS   (  63-)  A      0
  87 SER   (  84-)  A      0
  89 MSE   (  86-)  A      0
  96 MSE   (  93-)  A      0
 108 GLU   ( 105-)  A      0
 111 GLU   ( 108-)  A      0
 114 ASP   ( 111-)  A      0
 115 TRP   ( 112-)  A      0
 121 MSE   ( 118-)  A      0
 132 LEU   ( 129-)  A      0
 134 PHE   ( 131-)  A      0
 140 PRO   ( 137-)  A      0
And so on for a total of 376 lines.

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]

 383 PRO   (  80-)  B    0.17 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].

 255 PRO   ( 256-)  A   -64.6 envelop C-beta (-72 degrees)
 555 PRO   ( 265-)  B   -53.7 half-chair C-beta/C-alpha (-54 degrees)
 959 PRO   (  80-)  D  -123.9 half-chair C-delta/C-gamma (-126 degrees)
1016 PRO   ( 137-)  D  -122.2 half-chair C-delta/C-gamma (-126 degrees)
1100 PRO   ( 221-)  D  -124.3 half-chair C-delta/C-gamma (-126 degrees)
1135 PRO   ( 256-)  D   -64.5 envelop C-beta (-72 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.

 461 VAL   ( 162-)  B      CG1 <->  462 PHE   ( 163-)  B      N      0.47    2.53  INTRA BF
1146 MSE   ( 267-)  D      CE  <-> 1166 LEU   ( 287-)  D      CD2    0.41    2.79  INTRA BF
 745 SER   ( 157-)  C      O   <->  748 GLU   ( 160-)  C      CG     0.36    2.44  INTRA BF
 439 LYS   ( 136-)  B      NZ  <-> 1187 ATP   ( 311-)  B      N7     0.32    2.68  INTRA BF
 143 VAL   ( 144-)  A      CG2 <->  146 LYS   ( 147-)  A      NZ     0.28    2.82  INTRA BF
 735 LYS   ( 147-)  C      CD  <->  746 MSE   ( 158-)  C     SE      0.28    2.92  INTRA BF
 693 LYS   (  99-)  C      NZ  <->  703 THR   ( 109-)  C    A CG2    0.28    2.82  INTRA BL
 716 ASN   ( 122-)  C      ND2 <->  719 GLU   ( 125-)  C      CD     0.26    2.84  INTRA BF
 978 LYS   (  99-)  D      NZ  <-> 1051 GLU   ( 172-)  D      OE2    0.25    2.45  INTRA BL
1195 EDO   ( 313-)  D      C1  <-> 1201 HOH   ( 747 )  D      O      0.25    2.55  INTRA BF
 461 VAL   ( 162-)  B      O   <->  464 TRP   ( 165-)  B      N      0.23    2.47  INTRA BF
1185 ATP   ( 311-)  A      O1G <-> 1198 HOH   ( 646 )  A      O      0.23    2.17  INTRA BL
 840 MSE   ( 267-)  C      CE  <->  864 ILE   ( 291-)  C      CD1    0.22    2.98  INTRA BL
 446 LYS   ( 147-)  B      NZ  <->  464 TRP   ( 165-)  B      CH2    0.22    2.88  INTRA BF
 982 ARG   ( 103-)  D      NE  <-> 1201 HOH   ( 397 )  D      O      0.22    2.48  INTRA BL
 975 ASN   (  96-)  D      ND2 <->  993 GLU   ( 114-)  D      CD     0.22    2.88  INTRA BF
 346 LYS   (  43-)  B      NZ  <-> 1199 HOH   ( 353 )  B      O      0.21    2.49  INTRA BF
1190 ATP   ( 311-)  C      O1A <-> 1200 HOH   ( 536 )  C      O      0.20    2.20  INTRA BF
 452 ASP   ( 153-)  B      O   <->  456 SER   ( 157-)  B      OG     0.20    2.20  INTRA BF
 707 ILE   ( 113-)  C      CG2 <->  708 GLU   ( 114-)  C      N      0.19    2.81  INTRA BF
 730 LYS   ( 136-)  C      NZ  <-> 1190 ATP   ( 311-)  C      N7     0.19    2.81  INTRA BF
 103 LYS   ( 100-)  A      NZ  <->  408 GLU   ( 105-)  B      OE2    0.19    2.51  INTRA BL
  46 LYS   (  43-)  A      NZ  <-> 1198 HOH   ( 660 )  A      O      0.18    2.52  INTRA BF
1182 GLY   ( 303-)  D      C   <-> 1183 PHE   ( 304-)  D      CD1    0.18    2.92  INTRA BF
 716 ASN   ( 122-)  C      ND2 <->  719 GLU   ( 125-)  C      OE2    0.18    2.52  INTRA BF
And so on for a total of 146 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 753 TRP   ( 165-)  C      -6.44
 464 TRP   ( 165-)  B      -6.10
 475 LYS   ( 176-)  B      -6.06
 175 LYS   ( 176-)  A      -6.02
   2 ASN   (  -1-)  A      -5.84
 149 TYR   ( 150-)  A      -5.82
1044 TRP   ( 165-)  D      -5.82
 764 LYS   ( 176-)  C      -5.82
1083 TYR   ( 204-)  D      -5.79
 164 TRP   ( 165-)  A      -5.67
 449 TYR   ( 150-)  B      -5.58
1055 LYS   ( 176-)  D      -5.58
 738 TYR   ( 150-)  C      -5.50
 203 TYR   ( 204-)  A      -5.41
 173 TYR   ( 174-)  A      -5.25
1029 TYR   ( 150-)  D      -5.24
 256 TYR   ( 257-)  A      -5.13
 635 ASN   (  41-)  C      -5.05
 592 GLU   ( 302-)  B      -5.03
 874 GLU   ( 301-)  C      -5.03
 218 GLU   ( 219-)  A      -5.03
 301 GLU   ( 302-)  A      -5.03
1180 GLU   ( 301-)  D      -5.02
1053 TYR   ( 174-)  D      -5.00

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.

 173 TYR   ( 174-)  A       175 - LYS    176- ( A)         -5.32
 473 TYR   ( 174-)  B       475 - LYS    176- ( B)         -5.16
 762 TYR   ( 174-)  C       764 - LYS    176- ( C)         -5.05
1053 TYR   ( 174-)  D      1055 - LYS    176- ( D)         -4.98

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 918 THR   (  39-)  D   -2.86
 342 THR   (  39-)  B   -2.66
 554 LEU   ( 264-)  B   -2.54

Warning: Abnormal packing Z-score for sequential residues

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

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

 460 THR   ( 161-)  B     -  463 GLU   ( 164-)  B        -1.78

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1198 HOH   ( 444 )  A      O     53.78   79.36   52.88
1199 HOH   ( 439 )  B      O     27.91   40.35   30.12

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.

1198 HOH   ( 334 )  A      O
1198 HOH   ( 336 )  A      O
1198 HOH   ( 406 )  A      O
1198 HOH   ( 408 )  A      O
1198 HOH   ( 417 )  A      O
1198 HOH   ( 434 )  A      O
1199 HOH   ( 349 )  B      O
1199 HOH   ( 397 )  B      O
1200 HOH   ( 349 )  C      O
1200 HOH   ( 353 )  C      O
1200 HOH   ( 385 )  C      O
1200 HOH   ( 608 )  C      O
1201 HOH   ( 307 )  D      O
1201 HOH   ( 359 )  D      O
1201 HOH   ( 416 )  D      O
1201 HOH   ( 419 )  D      O
1201 HOH   ( 456 )  D      O
1201 HOH   ( 475 )  D      O
1201 HOH   ( 479 )  D      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.

 325 ASN   (  22-)  B
 621 ASN   (  27-)  C
 732 ASN   ( 138-)  C
 842 GLN   ( 269-)  C
 940 HIS   (  61-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  55 ASP   (  52-)  A    A N
  63 LEU   (  60-)  A      N
  84 TYR   (  81-)  A      N
  99 ASN   (  96-)  A    A N
 128 GLU   ( 125-)  A      N
 139 LYS   ( 136-)  A      NZ
 150 ASP   ( 151-)  A      N
 174 ILE   ( 175-)  A      N
 186 GLY   ( 187-)  A      N
 197 ALA   ( 198-)  A      N
 335 LYS   (  32-)  B      N
 363 LEU   (  60-)  B      N
 384 TYR   (  81-)  B      N
 419 THR   ( 116-)  B      N
 421 MSE   ( 118-)  B      N
 428 GLU   ( 125-)  B      N
 429 LEU   ( 126-)  B      N
 439 LYS   ( 136-)  B      NZ
 443 GLY   ( 140-)  B      N
 450 ASP   ( 151-)  B      N
 467 GLU   ( 168-)  B      N
 474 ILE   ( 175-)  B      N
 486 GLY   ( 187-)  B      N
 512 ALA   ( 222-)  B      N
 573 HIS   ( 283-)  B      N
And so on for a total of 59 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.

 425 ASN   ( 122-)  B      OD1
 754 ASP   ( 166-)  C      OD1
 760 GLU   ( 172-)  C      OE1
 760 GLU   ( 172-)  C      OE2
 833 GLU   ( 260-)  C      OE1
 892 GLU   (  13-)  D    A OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1186  CA   ( 310-)  B   -.-  -.-  Low probability ion. B=102.0
1188  CA   ( 312-)  B     0.41   1.04 Could be  K
1189  CA   ( 310-)  C   -.-  -.-  Low probability ion. B= 82.4
1191  CA   ( 312-)  C     0.49   1.52 Scores about as good as  K
1192  MG   ( 313-)  C     0.42   0.85 Is perhaps NA
1193  CA   ( 310-)  D     0.81   1.04 Scores about as good as NA
1194  CA   ( 312-)  D     0.64   0.86 Scores about as good as NA

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.

1198 HOH   ( 401 )  A      O  0.85  K  4
1200 HOH   ( 362 )  C      O  0.98  K  4 ION-B H2O-B
1200 HOH   ( 493 )  C      O  1.12  K  4 NCS 1/1
1200 HOH   ( 538 )  C      O  1.01  K  6 Ion-B H2O-B
1200 HOH   ( 749 )  C      O  0.95 NA  5 Ion-B
1201 HOH   ( 395 )  D      O  1.15  K  4
1201 HOH   ( 412 )  D      O  1.09  K  4 H2O-B
1201 HOH   ( 671 )  D      O  0.94  K  6

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.

  48 ASP   (  45-)  A   H-bonding suggests Asn
  55 ASP   (  52-)  A   H-bonding suggests Asn; but Alt-Rotamer
  78 GLU   (  75-)  A   H-bonding suggests Gln; but Alt-Rotamer
 130 ASP   ( 127-)  A   H-bonding suggests Asn
 316 GLU   (  13-)  B   H-bonding suggests Gln
 348 ASP   (  45-)  B   H-bonding suggests Asn
 351 GLU   (  48-)  B   H-bonding suggests Gln
 422 GLU   ( 119-)  B   H-bonding suggests Gln
 427 ASP   ( 124-)  B   H-bonding suggests Asn; but Alt-Rotamer
 465 ASP   ( 166-)  B   H-bonding suggests Asn; but Alt-Rotamer
 516 GLU   ( 226-)  B   H-bonding suggests Gln
 607 GLU   (  13-)  C   H-bonding suggests Gln
 636 GLU   (  42-)  C   H-bonding suggests Gln; but Alt-Rotamer
 639 ASP   (  45-)  C   H-bonding suggests Asn; but Alt-Rotamer
 642 GLU   (  48-)  C   H-bonding suggests Gln
 669 GLU   (  75-)  C   H-bonding suggests Gln; but Alt-Rotamer
 714 ASP   ( 120-)  C   H-bonding suggests Asn
 719 GLU   ( 125-)  C   H-bonding suggests Gln
 721 ASP   ( 127-)  C   H-bonding suggests Asn
 748 GLU   ( 160-)  C   H-bonding suggests Gln
 752 GLU   ( 164-)  C   H-bonding suggests Gln
 766 GLU   ( 178-)  C   H-bonding suggests Gln
 799 GLU   ( 226-)  C   H-bonding suggests Gln
 927 GLU   (  48-)  D   H-bonding suggests Gln
 954 GLU   (  75-)  D   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1006 ASP   ( 127-)  D   H-bonding suggests Asn
1045 ASP   ( 166-)  D   H-bonding suggests Asn; but Alt-Rotamer
1095 GLU   ( 216-)  D   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.259
  2nd generation packing quality :  -1.431
  Ramachandran plot appearance   :   0.269
  chi-1/chi-2 rotamer normality  :  -2.213
  Backbone conformation          :   0.783

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.443 (tight)
  Bond angles                    :   0.587 (tight)
  Omega angle restraints         :   0.938
  Side chain planarity           :   0.414 (tight)
  Improper dihedral distribution :   0.774
  B-factor distribution          :   1.097
  Inside/Outside distribution    :   1.023

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.443 (tight)
  Bond angles                    :   0.587 (tight)
  Omega angle restraints         :   0.938
  Side chain planarity           :   0.414 (tight)
  Improper dihedral distribution :   0.774
  B-factor distribution          :   1.097
  Inside/Outside distribution    :   1.023
==============

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.