WHAT IF Check report

This file was created 2012-03-27 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 pdb3q7d.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 : 0.444
CA-only RMS fit for the two chains : 0.226

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 NPX   (1591-)  A  -
1114 BOG   (   3-)  A  -
1115 BOG   (   6-)  A  -
1116 BOG   ( 620-)  A  -
1119 BOG   (   3-)  B  -
1122 BOG   ( 620-)  B  -
1123 NPX   (1591-)  B  -

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: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

  91 TYR   ( 122-)  A
 103 TYR   ( 134-)  A
 223 TYR   ( 254-)  A
 317 TYR   ( 348-)  A
 342 TYR   ( 373-)  A
 371 TYR   ( 402-)  A
 464 TYR   ( 495-)  A
 655 TYR   ( 134-)  B
 657 TYR   ( 136-)  B
 775 TYR   ( 254-)  B
 869 TYR   ( 348-)  B
 894 TYR   ( 373-)  B
1016 TYR   ( 495-)  B

Warning: Phenylalanine convention problem

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

  64 PHE   (  96-)  A
  76 PHE   ( 107-)  A
 167 PHE   ( 198-)  A
 178 PHE   ( 209-)  A
 189 PHE   ( 220-)  A
 391 PHE   ( 422-)  A
 447 PHE   ( 478-)  A
 616 PHE   (  96-)  B
 628 PHE   ( 107-)  B
 719 PHE   ( 198-)  B
 722 PHE   ( 201-)  B
 730 PHE   ( 209-)  B
 741 PHE   ( 220-)  B
 999 PHE   ( 478-)  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.

 142 ASP   ( 173-)  A
 237 ASP   ( 268-)  A
 484 ASP   ( 515-)  A

Warning: Glutamic acid convention problem

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

 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 493 GLU   ( 524-)  A
 691 GLU   ( 170-)  B
 697 GLU   ( 176-)  B
 802 GLU   ( 281-)  B
 860 GLU   ( 339-)  B
 978 GLU   ( 457-)  B
1007 GLU   ( 486-)  B
1011 GLU   ( 490-)  B
1045 GLU   ( 524-)  B

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.999401 -0.000199  0.000032|
 | -0.000199  0.999106  0.000096|
 |  0.000032  0.000096  0.998242|
Proposed new scale matrix

 |  0.008153  0.000002  0.000000|
 |  0.000001  0.007524  0.000000|
 |  0.000000  0.000000  0.005534|
With corresponding cell

    A    = 122.656  B   = 132.913  C    = 180.710
    Alpha=  90.002  Beta=  90.002  Gamma=  90.023

The CRYST1 cell dimensions

    A    = 122.735  B   = 133.028  C    = 181.039
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 49.288
(Under-)estimated Z-score: 5.174

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.

 106 LYS   ( 137-)  A      N    CA   C   124.50    4.8
 256 VAL   ( 287-)  A      N    CA   C   125.11    5.0
 257 GLY   ( 288-)  A     -C    N    CA  112.38   -4.8
 345 ARG   ( 376-)  A      CG   CD   NE  102.85   -4.5
 650 THR   ( 129-)  B      C    CA   CB  102.15   -4.2
 653 VAL   ( 132-)  B      C    CA   CB  102.15   -4.2
 808 VAL   ( 287-)  B      N    CA   C   124.59    4.8

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.

 142 ASP   ( 173-)  A
 237 ASP   ( 268-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 426 GLU   ( 457-)  A
 455 GLU   ( 486-)  A
 459 GLU   ( 490-)  A
 484 ASP   ( 515-)  A
 493 GLU   ( 524-)  A
 691 GLU   ( 170-)  B
 697 GLU   ( 176-)  B
 802 GLU   ( 281-)  B
 860 GLU   ( 339-)  B
 978 GLU   ( 457-)  B
1007 GLU   ( 486-)  B
1011 GLU   ( 490-)  B
1045 GLU   ( 524-)  B

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.

 942 GLN   ( 421-)  B    7.16
 390 GLN   ( 421-)  A    7.09
 256 VAL   ( 287-)  A    5.82
 808 VAL   ( 287-)  B    5.62
 106 LYS   ( 137-)  A    5.07
 150 VAL   ( 181-)  A    4.01

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.

 930 TYR   ( 409-)  B    -3.2
1035 PRO   ( 514-)  B    -3.1
 483 PRO   ( 514-)  A    -3.1
 564 ARG   (  44-)  B    -3.1
  12 ARG   (  44-)  A    -2.8
  64 PHE   (  96-)  A    -2.8
 616 PHE   (  96-)  B    -2.8
 119 ARG   ( 150-)  A    -2.6
 706 ARG   ( 185-)  B    -2.6
 602 LEU   (  82-)  B    -2.5
 802 GLU   ( 281-)  B    -2.5
 919 GLU   ( 398-)  B    -2.5
 367 GLU   ( 398-)  A    -2.5
 658 LYS   ( 137-)  B    -2.5
 906 TYR   ( 385-)  B    -2.4
 808 VAL   ( 287-)  B    -2.4
 581 ARG   (  61-)  B    -2.4
  29 ARG   (  61-)  A    -2.4
 943 PHE   ( 422-)  B    -2.4
 453 GLU   ( 484-)  A    -2.4
1096 CYS   ( 575-)  B    -2.4
 147 LEU   ( 178-)  A    -2.4
 354 TYR   ( 385-)  A    -2.4
 547 THR   ( 578-)  A    -2.3
 732 LYS   ( 211-)  B    -2.3
And so on for a total of 53 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

   7 ASN   (  39-)  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
  99 TYR   ( 130-)  A  Poor phi/psi
 105 TYR   ( 136-)  A  omega poor
 107 SER   ( 138-)  A  Poor phi/psi
 116 TYR   ( 147-)  A  omega poor
 154 ARG   ( 185-)  A  Poor phi/psi
 188 GLY   ( 219-)  A  omega poor
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 226 ILE   ( 257-)  A  omega poor
 228 GLY   ( 259-)  A  omega poor
 239 GLN   ( 270-)  A  Poor phi/psi
 256 VAL   ( 287-)  A  Poor phi/psi
 257 GLY   ( 288-)  A  omega poor
 367 GLU   ( 398-)  A  Poor phi/psi
 368 ASP   ( 399-)  A  Poor phi/psi
 389 THR   ( 420-)  A  omega poor
 391 PHE   ( 422-)  A  Poor phi/psi
 440 SER   ( 471-)  A  Poor phi/psi
And so on for a total of 65 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 976 SER   ( 455-)  B    0.36
 424 SER   ( 455-)  A    0.38
 623 VAL   ( 103-)  B    0.39
 853 SER   ( 332-)  B    0.40
 301 SER   ( 332-)  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!

   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
  36 ASN   (  68-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  64 PHE   (  96-)  A      0
  91 TYR   ( 122-)  A      0
  94 ASP   ( 125-)  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
And so on for a total of 428 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!

 227 GLY   ( 258-)  A   3.23   14
 779 GLY   ( 258-)  B   3.16   13
 131 PRO   ( 162-)  A   1.58   10

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].

 249 PRO   ( 280-)  A  -131.5 half-chair C-delta/C-gamma (-126 degrees)
 443 PRO   ( 474-)  A  -119.1 half-chair C-delta/C-gamma (-126 degrees)
 483 PRO   ( 514-)  A   113.1 envelop C-beta (108 degrees)
 507 PRO   ( 538-)  A  -114.2 envelop C-gamma (-108 degrees)
 555 PRO   (  35-)  B  -120.9 half-chair C-delta/C-gamma (-126 degrees)
 693 PRO   ( 172-)  B  -116.7 envelop C-gamma (-108 degrees)
 784 PRO   ( 263-)  B   100.4 envelop C-beta (108 degrees)
 798 PRO   ( 277-)  B  -120.0 half-chair C-delta/C-gamma (-126 degrees)
 995 PRO   ( 474-)  B  -115.0 envelop C-gamma (-108 degrees)
1035 PRO   ( 514-)  B   145.5 envelop C-alpha (144 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 665 ASN   ( 144-)  B      ND2 <-> 1110 NAG   ( 671-)  B      C1     0.94    2.16  INTRA BL
 113 ASN   ( 144-)  A      ND2 <-> 1106 NAG   ( 671-)  A      C1     0.80    2.30  INTRA BL
  36 ASN   (  68-)  A      ND2 <-> 1105 NAG   ( 661-)  A      C1     0.68    2.42  INTRA BF
 659 SER   ( 138-)  B      N   <-> 1125 HOH   ( 756 )  B      O      0.67    2.03  INTRA BL
 651 TYR   ( 130-)  B      N   <-> 1125 HOH   ( 869 )  B      O      0.63    2.07  INTRA BL
 802 GLU   ( 281-)  B      O   <->  804 LEU   ( 283-)  B      N      0.63    2.07  INTRA BF
 931 ASN   ( 410-)  B      ND2 <-> 1111 NAG   ( 681-)  B      C1     0.62    2.48  INTRA BF
  99 TYR   ( 130-)  A      N   <-> 1124 HOH   ( 751 )  A      O      0.61    2.09  INTRA BL
 107 SER   ( 138-)  A      N   <-> 1124 HOH   ( 908 )  A      O      0.60    2.10  INTRA BL
 154 ARG   ( 185-)  A      CZ  <-> 1124 HOH   ( 801 )  A      O      0.53    2.27  INTRA
 671 ARG   ( 150-)  B      CB  <-> 1125 HOH   ( 829 )  B      O      0.51    2.29  INTRA BL
 843 GLU   ( 322-)  B      CG  <-> 1125 HOH   ( 722 )  B      O      0.50    2.30  INTRA
 671 ARG   ( 150-)  B      CG  <->  673 LEU   ( 152-)  B      O      0.50    2.30  INTRA BL
  98 THR   ( 129-)  A      C   <-> 1124 HOH   ( 751 )  A      O      0.50    2.30  INTRA BL
 346 ILE   ( 377-)  A      CB  <-> 1124 HOH   ( 677 )  A      O      0.48    2.32  INTRA BL
 379 ASN   ( 410-)  A      ND2 <-> 1107 NAG   ( 681-)  A      C1     0.47    2.63  INTRA BF
 650 THR   ( 129-)  B      C   <-> 1125 HOH   ( 869 )  B      O      0.46    2.34  INTRA BL
 809 GLY   ( 288-)  B      C   <-> 1125 HOH   ( 825 )  B      O      0.46    2.34  INTRA BL
 505 GLY   ( 536-)  A      C   <-> 1124 HOH   ( 809 )  A      O      0.45    2.35  INTRA BL
 588 ASN   (  68-)  B      ND2 <-> 1109 NAG   ( 661-)  B      C1     0.44    2.66  INTRA BF
 671 ARG   ( 150-)  B      NE  <-> 1125 HOH   ( 829 )  B      O      0.44    2.26  INTRA BL
 119 ARG   ( 150-)  A      NH2 <->  427 MET   ( 458-)  A      O      0.44    2.26  INTRA BL
1000 GLU   ( 479-)  B      CB  <-> 1006 LYS   ( 485-)  B      NZ     0.43    2.67  INTRA
 154 ARG   ( 185-)  A      NH1 <-> 1114 BOG   (   3-)  A      C5'    0.42    2.68  INTRA
 663 PHE   ( 142-)  B      O   <->  897 ARG   ( 376-)  B      NH2    0.41    2.29  INTRA BL
And so on for a total of 283 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 247 HIS   ( 278-)  A      -6.70
  29 ARG   (  61-)  A      -6.67
 581 ARG   (  61-)  B      -6.52
 799 HIS   ( 278-)  B      -6.51
 546 PHE   ( 577-)  A      -6.15
 572 PHE   (  52-)  B      -6.10
  20 PHE   (  52-)  A      -6.00
 386 HIS   ( 417-)  A      -5.72
  33 TYR   (  65-)  A      -5.62
 378 TYR   ( 409-)  A      -5.60
 938 HIS   ( 417-)  B      -5.57
 138 LYS   ( 169-)  A      -5.47
 154 ARG   ( 185-)  A      -5.42
 339 GLN   ( 370-)  A      -5.38
 690 LYS   ( 169-)  B      -5.31
 397 ARG   ( 428-)  A      -5.29
 185 ARG   ( 216-)  A      -5.26
 949 ARG   ( 428-)  B      -5.23
 891 GLN   ( 370-)  B      -5.22
 244 TYR   ( 275-)  A      -5.19
 184 LYS   ( 215-)  A      -5.16
 585 TYR   (  65-)  B      -5.16
 736 LYS   ( 215-)  B      -5.10
 708 PHE   ( 187-)  B      -5.02
 102 HIS   ( 133-)  A      -5.02
 796 TYR   ( 275-)  B      -5.01

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.

 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -4.88
 690 LYS   ( 169-)  B       692 - LEU    171- ( B)         -4.86

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.

 886 LEU   ( 365-)  B   -2.73
 105 TYR   ( 136-)  A   -2.58
  92 LEU   ( 123-)  A   -2.56
 334 LEU   ( 365-)  A   -2.54
 644 LEU   ( 123-)  B   -2.54

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.

1124 HOH   ( 887 )  A      O    -11.02   45.12   74.42
1124 HOH   ( 911 )  A      O    -35.67   79.47   57.03
1124 HOH   ( 918 )  A      O    -39.86   75.11   51.76
1125 HOH   ( 803 )  B      O    -19.48   34.85    5.71
1125 HOH   ( 883 )  B      O    -69.00   34.21   38.50
1125 HOH   ( 885 )  B      O    -68.29   31.03   37.93
1125 HOH   ( 917 )  B      O    -71.27   39.99   36.21

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.

1124 HOH   ( 756 )  A      O
1124 HOH   ( 785 )  A      O
1124 HOH   ( 819 )  A      O
1124 HOH   ( 881 )  A      O
1124 HOH   ( 883 )  A      O
1124 HOH   ( 884 )  A      O
1124 HOH   ( 889 )  A      O
1124 HOH   ( 902 )  A      O
1124 HOH   ( 903 )  A      O
1124 HOH   ( 909 )  A      O
1124 HOH   ( 910 )  A      O
1124 HOH   ( 911 )  A      O
1125 HOH   ( 678 )  B      O
1125 HOH   ( 756 )  B      O
1125 HOH   ( 757 )  B      O
1125 HOH   ( 826 )  B      O
1125 HOH   ( 831 )  B      O
1125 HOH   ( 842 )  B      O
1125 HOH   ( 846 )  B      O
1125 HOH   ( 855 )  B      O
1125 HOH   ( 873 )  B      O
1125 HOH   ( 879 )  B      O
1125 HOH   ( 880 )  B      O
Marked this atom as acceptor 1118  CL  (   1-) A     CL
Marked this atom as acceptor 1121  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.

  10 GLN   (  42-)  A
  63 HIS   (  95-)  A
 102 HIS   ( 133-)  A
 173 HIS   ( 204-)  A
 201 HIS   ( 232-)  A
 289 HIS   ( 320-)  A
 319 GLN   ( 350-)  A
 320 HIS   ( 351-)  A
 355 HIS   ( 386-)  A
 380 ASN   ( 411-)  A
 386 HIS   ( 417-)  A
 433 ASN   ( 464-)  A
 550 ASN   ( 581-)  A
 562 GLN   (  42-)  B
 625 ASN   ( 105-)  B
 654 HIS   ( 133-)  B
 725 HIS   ( 204-)  B
 735 HIS   ( 214-)  B
 753 HIS   ( 232-)  B
 763 HIS   ( 242-)  B
 803 ASN   ( 282-)  B
 841 HIS   ( 320-)  B
 871 GLN   ( 350-)  B
 872 HIS   ( 351-)  B
 877 HIS   ( 356-)  B
 932 ASN   ( 411-)  B
 938 HIS   ( 417-)  B
 985 ASN   ( 464-)  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.

  22 GLN   (  54-)  A      N
  76 PHE   ( 107-)  A      N
 105 TYR   ( 136-)  A      N
 106 LYS   ( 137-)  A      NZ
 107 SER   ( 138-)  A      N
 107 SER   ( 138-)  A      OG
 137 ASN   ( 168-)  A      N
 154 ARG   ( 185-)  A      NE
 154 ARG   ( 185-)  A      NH1
 154 ARG   ( 185-)  A      NH2
 172 GLN   ( 203-)  A      NE2
 177 GLN   ( 208-)  A      NE2
 181 THR   ( 212-)  A      N
 205 GLU   ( 236-)  A      N
 209 ARG   ( 240-)  A      NH2
 217 LYS   ( 248-)  A      N
 251 ASN   ( 282-)  A      N
 264 VAL   ( 295-)  A      N
 266 GLY   ( 297-)  A      N
 276 ARG   ( 307-)  A      NH1
 326 PHE   ( 357-)  A      N
 345 ARG   ( 376-)  A      NH1
 373 PHE   ( 404-)  A      N
 394 SER   ( 425-)  A      N
 407 ARG   ( 438-)  A      NH2
And so on for a total of 70 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.

 211 HIS   ( 242-)  A      ND1
 308 GLU   ( 339-)  A      OE2
 351 ASN   ( 382-)  A      OD1
 942 GLN   ( 421-)  B      OE1
1045 GLU   ( 524-)  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.

1124 HOH   ( 625 )  A      O  1.04  K  4
1124 HOH   ( 628 )  A      O  1.00  K  5
1124 HOH   ( 762 )  A      O  1.14  K  5
1124 HOH   ( 778 )  A      O  1.02  K  4
1125 HOH   (  26 )  B      O  0.90  K  4

Warning: Possible wrong residue type

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

 139 GLU   ( 170-)  A   H-bonding suggests Gln
 573 ASP   (  53-)  B   H-bonding suggests Asn
 691 GLU   ( 170-)  B   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.442
  2nd generation packing quality :  -1.893
  Ramachandran plot appearance   :  -1.500
  chi-1/chi-2 rotamer normality  :  -2.456
  Backbone conformation          :  -0.926

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.365 (tight)
  Bond angles                    :   0.648 (tight)
  Omega angle restraints         :   1.068
  Side chain planarity           :   0.383 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   1.097
  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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.365 (tight)
  Bond angles                    :   0.648 (tight)
  Omega angle restraints         :   1.068
  Side chain planarity           :   0.383 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   1.097
  Inside/Outside distribution    :   1.109
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
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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.