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 pdb3nt1.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.456
CA-only RMS fit for the two chains : 0.173

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Warning: 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.

1113 BOG   (   3-)  A  -
1114 NPS   (   5-)  A  -
1115 BOG   (   6-)  A  -
1116 BOG   ( 620-)  A  -
1121 BOG   (   3-)  B  -
1122 NPS   (   4-)  B  -

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.

 288 GLU   ( 319-)  A  -

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.

 288 GLU   ( 319-)  A  -

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1106 NAG   ( 671-)  A  -   O4  bound to 1107 NAG   ( 672-)  A  -   C1
1109 NAG   ( 671-)  B  -   O4  bound to 1110 NAG   ( 672-)  B  -   C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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: 2

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 191 ARG   ( 222-)  A

Warning: Tyrosine convention problem

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

  23 TYR   (  55-)  A
  33 TYR   (  65-)  A
  59 TYR   (  91-)  A
  99 TYR   ( 130-)  A
 103 TYR   ( 134-)  A
 116 TYR   ( 147-)  A
 223 TYR   ( 254-)  A
 231 TYR   ( 262-)  A
 244 TYR   ( 275-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 444 TYR   ( 475-)  A
 464 TYR   ( 495-)  A
 513 TYR   ( 544-)  A
 575 TYR   (  55-)  B
 585 TYR   (  65-)  B
 611 TYR   (  91-)  B
 651 TYR   ( 130-)  B
 655 TYR   ( 134-)  B
 668 TYR   ( 147-)  B
 775 TYR   ( 254-)  B
 783 TYR   ( 262-)  B
 796 TYR   ( 275-)  B
 894 TYR   ( 373-)  B
 906 TYR   ( 385-)  B
 996 TYR   ( 475-)  B
1065 TYR   ( 544-)  B

Warning: Phenylalanine convention problem

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

  20 PHE   (  52-)  A
  64 PHE   (  96-)  A
 156 PHE   ( 187-)  A
 170 PHE   ( 201-)  A
 216 PHE   ( 247-)  A
 254 PHE   ( 285-)  A
 336 PHE   ( 367-)  A
 439 PHE   ( 470-)  A
 447 PHE   ( 478-)  A
 498 PHE   ( 529-)  A
 519 PHE   ( 550-)  A
 549 PHE   ( 580-)  A
 572 PHE   (  52-)  B
 616 PHE   (  96-)  B
 708 PHE   ( 187-)  B
 722 PHE   ( 201-)  B
 768 PHE   ( 247-)  B
 806 PHE   ( 285-)  B
 888 PHE   ( 367-)  B
 916 PHE   ( 395-)  B
 991 PHE   ( 470-)  B
 999 PHE   ( 478-)  B
1050 PHE   ( 529-)  B
1071 PHE   ( 550-)  B
1101 PHE   ( 580-)  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.

  21 ASP   (  53-)  A
 127 ASP   ( 158-)  A
 142 ASP   ( 173-)  A
 208 ASP   ( 239-)  A
 218 ASP   ( 249-)  A
 237 ASP   ( 268-)  A
 362 ASP   ( 393-)  A
 368 ASP   ( 399-)  A
 466 ASP   ( 497-)  A
 573 ASP   (  53-)  B
 679 ASP   ( 158-)  B
 694 ASP   ( 173-)  B
 760 ASP   ( 239-)  B
 770 ASP   ( 249-)  B
 789 ASP   ( 268-)  B
 914 ASP   ( 393-)  B
 920 ASP   ( 399-)  B
1018 ASP   ( 497-)  B

Warning: Glutamic acid convention problem

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

 109 GLU   ( 140-)  A
 145 GLU   ( 176-)  A
 205 GLU   ( 236-)  A
 241 GLU   ( 272-)  A
 250 GLU   ( 281-)  A
 277 GLU   ( 308-)  A
 291 GLU   ( 322-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 367 GLU   ( 398-)  A
 370 GLU   ( 401-)  A
 393 GLU   ( 424-)  A
 426 GLU   ( 457-)  A
 449 GLU   ( 480-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 471 GLU   ( 502-)  A
 489 GLU   ( 520-)  A
 661 GLU   ( 140-)  B
 697 GLU   ( 176-)  B
 757 GLU   ( 236-)  B
 793 GLU   ( 272-)  B
 802 GLU   ( 281-)  B
 829 GLU   ( 308-)  B
 843 GLU   ( 322-)  B
 860 GLU   ( 339-)  B
 885 GLU   ( 364-)  B
 919 GLU   ( 398-)  B
 922 GLU   ( 401-)  B
 945 GLU   ( 424-)  B
 978 GLU   ( 457-)  B
1001 GLU   ( 480-)  B
1005 GLU   ( 484-)  B
1007 GLU   ( 486-)  B
1011 GLU   ( 490-)  B
1041 GLU   ( 520-)  B

Geometric checks

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.327
RMS-deviation in bond distances: 0.008

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

 |  0.997606 -0.000227 -0.000100|
 | -0.000227  0.997636  0.000141|
 | -0.000100  0.000141  0.997913|
Proposed new scale matrix

 |  0.008197  0.000002  0.000000|
 |  0.000002  0.007524 -0.000001|
 |  0.000000  0.000000  0.005529|
With corresponding cell

    A    = 122.001  B   = 132.912  C    = 180.880
    Alpha=  89.993  Beta=  90.002  Gamma=  90.026

The CRYST1 cell dimensions

    A    = 122.295  B   = 133.233  C    = 181.269
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 197.272
(Under-)estimated Z-score: 10.351

Warning: Low bond angle variability

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

RMS Z-score for bond angles: 0.565
RMS-deviation in bond angles: 1.173

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.

  21 ASP   (  53-)  A
 109 GLU   ( 140-)  A
 127 ASP   ( 158-)  A
 142 ASP   ( 173-)  A
 145 GLU   ( 176-)  A
 191 ARG   ( 222-)  A
 205 GLU   ( 236-)  A
 208 ASP   ( 239-)  A
 218 ASP   ( 249-)  A
 237 ASP   ( 268-)  A
 241 GLU   ( 272-)  A
 250 GLU   ( 281-)  A
 277 GLU   ( 308-)  A
 291 GLU   ( 322-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 367 GLU   ( 398-)  A
 368 ASP   ( 399-)  A
 370 GLU   ( 401-)  A
 393 GLU   ( 424-)  A
 426 GLU   ( 457-)  A
 449 GLU   ( 480-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
And so on for a total of 55 lines.

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.

 150 VAL   ( 181-)  A    4.48
 702 VAL   ( 181-)  B    4.15

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.

 616 PHE   (  96-)  B    -2.5
  64 PHE   (  96-)  A    -2.5
 906 TYR   ( 385-)  B    -2.5
 354 TYR   ( 385-)  A    -2.5
 239 GLN   ( 270-)  A    -2.4
 453 GLU   ( 484-)  A    -2.4
1099 THR   ( 578-)  B    -2.3
  12 ARG   (  44-)  A    -2.3
 440 SER   ( 471-)  A    -2.3
 133 GLY   ( 164-)  A    -2.2
 685 GLY   ( 164-)  B    -2.2
1005 GLU   ( 484-)  B    -2.2
 547 THR   ( 578-)  A    -2.1
 751 LEU   ( 230-)  B    -2.1
 199 LEU   ( 230-)  A    -2.1
1019 ILE   ( 498-)  B    -2.1
 992 SER   ( 471-)  B    -2.1
 812 VAL   ( 291-)  B    -2.1
 260 VAL   ( 291-)  A    -2.1
 467 ILE   ( 498-)  A    -2.1
 791 GLN   ( 270-)  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.

   7 ASN   (  39-)  A  Poor phi/psi
  11 ASN   (  43-)  A  Poor phi/psi
  12 ARG   (  44-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  37 CYS   (  69-)  A  Poor phi/psi
  64 PHE   (  96-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 111 PHE   ( 142-)  A  omega poor
 116 TYR   ( 147-)  A  omega poor
 154 ARG   ( 185-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 219 GLY   ( 250-)  A  omega poor
 239 GLN   ( 270-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
 440 SER   ( 471-)  A  Poor phi/psi
 465 SER   ( 496-)  A  Poor phi/psi
 481 PRO   ( 512-)  A  omega poor
 563 ASN   (  43-)  B  Poor phi/psi
 564 ARG   (  44-)  B  Poor phi/psi
 581 ARG   (  61-)  B  Poor phi/psi
 589 CYS   (  69-)  B  Poor phi/psi
 616 PHE   (  96-)  B  Poor phi/psi
 647 SER   ( 126-)  B  PRO omega poor
 650 THR   ( 129-)  B  Poor phi/psi
 668 TYR   ( 147-)  B  omega poor
 686 VAL   ( 165-)  B  Poor phi/psi
 706 ARG   ( 185-)  B  Poor phi/psi
 730 PHE   ( 209-)  B  omega poor
 751 LEU   ( 230-)  B  Poor phi/psi
 768 PHE   ( 247-)  B  Poor phi/psi
 770 ASP   ( 249-)  B  Poor phi/psi
 771 GLY   ( 250-)  B  omega poor
 791 GLN   ( 270-)  B  Poor phi/psi
 919 GLU   ( 398-)  B  Poor phi/psi
 980 LYS   ( 459-)  B  Poor phi/psi
 992 SER   ( 471-)  B  Poor phi/psi
1017 SER   ( 496-)  B  Poor phi/psi
1033 PRO   ( 512-)  B  omega poor
 chi-1/chi-2 correlation Z-score : 0.068

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.

 976 SER   ( 455-)  B    0.35
 420 SER   ( 451-)  A    0.36
 424 SER   ( 455-)  A    0.36
 631 SER   ( 110-)  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!

   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  12 ARG   (  44-)  A      0
  21 ASP   (  53-)  A      0
  22 GLN   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 PHE   (  64-)  A      0
  33 TYR   (  65-)  A      0
  35 GLU   (  67-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
  98 THR   ( 129-)  A      0
  99 TYR   ( 130-)  A      0
 102 HIS   ( 133-)  A      0
 105 TYR   ( 136-)  A      0
And so on for a total of 409 lines.

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!

 131 PRO   ( 162-)  A   1.70   13
 511 PRO   ( 542-)  A   1.56   15

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]

 410 PRO   ( 441-)  A    0.18 LOW
 511 PRO   ( 542-)  A    0.15 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].

 141 PRO   ( 172-)  A  -112.5 envelop C-gamma (-108 degrees)
1049 PRO   ( 528-)  B   103.1 envelop C-beta (108 degrees)
1063 PRO   ( 542-)  B  -127.3 half-chair C-delta/C-gamma (-126 degrees)
1068 PRO   ( 547-)  B  -138.0 envelop C-delta (-144 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 896 ASN   ( 375-)  B      ND2 <-> 1124 HOH   ( 832 )  B      O      0.49    2.21  INTRA
 357 HIS   ( 388-)  A      ND1 <-> 1123 HOH   ( 836 )  A      O      0.22    2.48  INTRA
 251 ASN   ( 282-)  A      ND2 <-> 1123 HOH   ( 946 )  A      O      0.22    2.48  INTRA
 185 ARG   ( 216-)  A      NH1 <-> 1107 NAG   ( 672-)  A      O7     0.21    2.49  INTRA
 357 HIS   ( 388-)  A      N   <->  358 PRO   ( 389-)  A      CD     0.19    2.81  INTRA BL
 735 HIS   ( 214-)  B      ND1 <-> 1124 HOH   (1030 )  B      O      0.18    2.52  INTRA
 909 HIS   ( 388-)  B      N   <->  910 PRO   ( 389-)  B      CD     0.17    2.83  INTRA BL
  55 ASN   (  87-)  A      ND2 <-> 1116 BOG   ( 620-)  A      C6     0.16    2.94  INTRA BF
 737 ARG   ( 216-)  B      NH1 <-> 1109 NAG   ( 671-)  B      O4     0.16    2.54  INTRA
 696 LYS   ( 175-)  B      NZ  <->  700 GLU   ( 179-)  B      OE2    0.15    2.55  INTRA
 717 MET   ( 196-)  B      CE  <->  952 ALA   ( 431-)  B      CB     0.13    3.07  INTRA
 520 GLY   ( 551-)  A      C   <->  568 MET   (  48-)  B      SD     0.11    3.29  INTRA
1005 GLU   ( 484-)  B      OE2 <-> 1008 MET   ( 487-)  B      N      0.11    2.59  INTRA
 252 LEU   ( 283-)  A      CD2 <->  384 LEU   ( 415-)  A      CD1    0.11    3.09  INTRA
  16 MET   (  48-)  A      SD  <-> 1072 GLY   ( 551-)  B      C      0.08    3.32  INTRA
 681 PRO   ( 160-)  B      O   <->  690 LYS   ( 169-)  B      NZ     0.07    2.63  INTRA BF
 296 GLN   ( 327-)  A      NE2 <-> 1123 HOH   ( 883 )  A      O      0.07    2.63  INTRA BL
 135 LYS   ( 166-)  A      NZ  <-> 1123 HOH   (1037 )  A      O      0.07    2.63  INTRA
 646 ASP   ( 125-)  B      OD2 <-> 1124 HOH   (1078 )  B      O      0.06    2.34  INTRA
 815 LEU   ( 294-)  B      O   <->  930 TYR   ( 409-)  B      N      0.06    2.64  INTRA
 559 ASN   (  39-)  B      N   <->  560 PRO   (  40-)  B      CD     0.06    2.94  INTRA
 603 LYS   (  83-)  B      NZ  <-> 1124 HOH   (1068 )  B      O      0.05    2.65  INTRA
 518 THR   ( 549-)  A      OG1 <->  658 LYS   ( 137-)  B      NZ     0.05    2.65  INTRA
 180 LYS   ( 211-)  A      NZ  <->  200 ASN   ( 231-)  A      OD1    0.05    2.65  INTRA BL
 219 GLY   ( 250-)  A      C   <->  282 CYS   ( 313-)  A      SG     0.04    3.36  INTRA BL
  14 GLU   (  46-)  A      OE1 <->  106 LYS   ( 137-)  A      NZ     0.04    2.66  INTRA
 848 GLN   ( 327-)  B      NE2 <-> 1124 HOH   (   5 )  B      O      0.03    2.67  INTRA BL
 357 HIS   ( 388-)  A      CE1 <->  416 VAL   ( 447-)  A      CG1    0.03    3.17  INTRA
 285 LEU   ( 316-)  A      O   <->  289 HIS   ( 320-)  A      N      0.03    2.67  INTRA BL
 903 ASN   ( 382-)  B      O   <->  907 HIS   ( 386-)  B      CD2    0.03    2.77  INTRA BL
 176 HIS   ( 207-)  A      NE2 <-> 1123 HOH   ( 943 )  A      O      0.03    2.67  INTRA
 355 HIS   ( 386-)  A      ND1 <->  420 SER   ( 451-)  A      OG     0.03    2.67  INTRA
 837 LEU   ( 316-)  B      O   <->  841 HIS   ( 320-)  B      N      0.03    2.67  INTRA BL
   7 ASN   (  39-)  A      N   <->    8 PRO   (  40-)  A      CD     0.02    2.98  INTRA
 881 LYS   ( 360-)  B      NZ  <-> 1124 HOH   (1097 )  B      O      0.02    2.68  INTRA
 221 LEU   ( 252-)  A      CB  <->  275 LEU   ( 306-)  A      CD1    0.02    3.18  INTRA BL
 195 HIS   ( 226-)  A      ND1 <->  346 ILE   ( 377-)  A      N      0.02    2.98  INTRA BL
 839 GLN   ( 318-)  B      NE2 <-> 1124 HOH   (1022 )  B      O      0.01    2.69  INTRA
 115 SER   ( 146-)  A      O   <->  190 THR   ( 221-)  A      N      0.01    2.69  INTRA BL
 717 MET   ( 196-)  B      CE  <->  952 ALA   ( 431-)  B      CA     0.01    3.19  INTRA
 173 HIS   ( 204-)  A      CD2 <->  261 PHE   ( 292-)  A      CE2    0.01    3.19  INTRA BL
  29 ARG   (  61-)  A      NH2 <-> 1063 PRO   ( 542-)  B      O      0.01    2.69  INTRA BL
 865 VAL   ( 344-)  B      O   <->  870 VAL   ( 349-)  B      N      0.01    2.69  INTRA BL
 725 HIS   ( 204-)  B      CD2 <->  813 PHE   ( 292-)  B      CE2    0.01    3.19  INTRA BL
 442 LYS   ( 473-)  A      NZ  <-> 1123 HOH   ( 981 )  A      O      0.01    2.69  INTRA

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 247 HIS   ( 278-)  A      -6.59
 799 HIS   ( 278-)  B      -6.57
 581 ARG   (  61-)  B      -6.51
  29 ARG   (  61-)  A      -6.39
  20 PHE   (  52-)  A      -6.17
 572 PHE   (  52-)  B      -5.99
 138 LYS   ( 169-)  A      -5.55
 397 ARG   ( 428-)  A      -5.51
 949 ARG   ( 428-)  B      -5.50
 185 ARG   ( 216-)  A      -5.41
 386 HIS   ( 417-)  A      -5.40
 154 ARG   ( 185-)  A      -5.36
 891 GLN   ( 370-)  B      -5.34
 938 HIS   ( 417-)  B      -5.33
 339 GLN   ( 370-)  A      -5.31
 737 ARG   ( 216-)  B      -5.26
 690 LYS   ( 169-)  B      -5.26
 585 TYR   (  65-)  B      -5.24
  33 TYR   (  65-)  A      -5.22
 736 LYS   ( 215-)  B      -5.21
 706 ARG   ( 185-)  B      -5.19
 156 PHE   ( 187-)  A      -5.12
 546 PHE   ( 577-)  A      -5.09
 753 HIS   ( 232-)  B      -5.08
 201 HIS   ( 232-)  A      -5.07
 708 PHE   ( 187-)  B      -5.07
 184 LYS   ( 215-)  A      -5.06
 540 ASN   ( 571-)  A      -5.06

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

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

 194 GLY   ( 225-)  A   -3.17
 657 TYR   ( 136-)  B   -2.88
 344 ASN   ( 375-)  A   -2.75
  92 LEU   ( 123-)  A   -2.68
 886 LEU   ( 365-)  B   -2.63
 334 LEU   ( 365-)  A   -2.60
 105 TYR   ( 136-)  A   -2.56

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

1123 HOH   ( 730 )  A      O    -61.28  -18.64  -60.00
1123 HOH   ( 737 )  A      O    -57.52  -27.69  -68.18
1123 HOH   (1116 )  A      O    -33.29   -3.86  -50.83
1124 HOH   (1107 )  B      O    -31.80  -47.70    7.22

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.

1123 HOH   ( 623 )  A      O
1123 HOH   ( 933 )  A      O
Bound group on Asn; dont flip   36 ASN  (  68-) A
Bound to: 1105 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 1106 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 1108 NAG  ( 681-) A
Bound group on Asn; dont flip  588 ASN  (  68-) B
Bound to: 1112 NAG  (   9-) B
Bound group on Asn; dont flip  665 ASN  ( 144-) B
Bound to: 1109 NAG  ( 671-) B
Bound group on Asn; dont flip  931 ASN  ( 410-) B
Bound to: 1111 NAG  ( 681-) B
Marked this atom as acceptor 1117  CL  (   1-) A     CL
Marked this atom as acceptor 1120  CL  (   1-) B     CL
Metal-coordinating Histidine residue 357 fixed to   1
Metal-coordinating Histidine residue 909 fixed to   1

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.

   7 ASN   (  39-)  A
 137 ASN   ( 168-)  A
 338 GLN   ( 369-)  A
 848 GLN   ( 327-)  B
 890 GLN   ( 369-)  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.

   2 ASN   (  34-)  A      N
  19 GLY   (  51-)  A      N
  95 SER   ( 126-)  A      OG
 100 ASN   ( 131-)  A      ND2
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 154 ARG   ( 185-)  A      NE
 154 ARG   ( 185-)  A      NH2
 172 GLN   ( 203-)  A      NE2
 177 GLN   ( 208-)  A      NE2
 181 THR   ( 212-)  A      N
 217 LYS   ( 248-)  A      N
 239 GLN   ( 270-)  A      NE2
 264 VAL   ( 295-)  A      N
 266 GLY   ( 297-)  A      N
 326 PHE   ( 357-)  A      N
 420 SER   ( 451-)  A      OG
 429 TYR   ( 460-)  A      OH
 446 SER   ( 477-)  A      N
 490 THR   ( 521-)  A      N
 553 ALA   (  33-)  B      N
 571 GLY   (  51-)  B      N
 574 GLN   (  54-)  B      N
 641 ARG   ( 120-)  B      NE
 652 ASN   ( 131-)  B      ND2
 657 TYR   ( 136-)  B      N
 657 TYR   ( 136-)  B      OH
 659 SER   ( 138-)  B      OG
 724 GLN   ( 203-)  B      NE2
 729 GLN   ( 208-)  B      NE2
 755 TYR   ( 234-)  B      OH
 769 LYS   ( 248-)  B      N
 776 GLN   ( 255-)  B      NE2
 816 VAL   ( 295-)  B      N
 818 GLY   ( 297-)  B      N
 878 PHE   ( 357-)  B      N
 903 ASN   ( 382-)  B      ND2
 909 HIS   ( 388-)  B      ND1
 998 SER   ( 477-)  B      N
1042 THR   ( 521-)  B      N
1109 NAG   ( 671-)  B      N2
Only metal coordination for  357 HIS  ( 388-) A      NE2
Only metal coordination for  909 HIS  ( 388-) B      NE2

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 172 GLN   ( 203-)  A      OE1
 308 GLU   ( 339-)  A      OE2
 724 GLN   ( 203-)  B      OE1

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.

1123 HOH   (   7 )  A      O  0.92  K  5
1123 HOH   (  29 )  A      O  0.91  K  5
1123 HOH   ( 733 )  A      O  0.91  K  4
1123 HOH   ( 776 )  A      O  0.85  K  6 Ion-B
1123 HOH   ( 830 )  A      O  0.98  K  5
1123 HOH   (1007 )  A      O  1.05  K  4 Ion-B
1124 HOH   ( 657 )  B      O  0.95  K  4
1124 HOH   ( 677 )  B      O  1.04  K  5
1124 HOH   ( 699 )  B      O  0.88  K  5
1124 HOH   ( 709 )  B      O  0.98  K  5
1124 HOH   ( 817 )  B      O  0.85  K  4
1124 HOH   ( 914 )  B      O  0.98  K  4
1124 HOH   ( 992 )  B      O  1.10  K  4 Ion-B

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.

  21 ASP   (  53-)  A   H-bonding suggests Asn
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 573 ASP   (  53-)  B   H-bonding suggests Asn
 843 GLU   ( 322-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.036
  2nd generation packing quality :  -1.279
  Ramachandran plot appearance   :   0.219
  chi-1/chi-2 rotamer normality  :   0.068
  Backbone conformation          :  -0.911

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.327 (tight)
  Bond angles                    :   0.565 (tight)
  Omega angle restraints         :   0.959
  Side chain planarity           :   0.390 (tight)
  Improper dihedral distribution :   0.541
  B-factor distribution          :   0.372
  Inside/Outside distribution    :   1.109

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.73


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.327 (tight)
  Bond angles                    :   0.565 (tight)
  Omega angle restraints         :   0.959
  Side chain planarity           :   0.390 (tight)
  Improper dihedral distribution :   0.541
  B-factor distribution          :   0.372
  Inside/Outside distribution    :   1.109
==============

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.