WHAT IF Check report

This file was created 2011-12-18 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 pdb3s4s.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 D

All-atom RMS fit for the two chains : 0.646
CA-only RMS fit for the two chains : 0.249

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 D

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: C and F

All-atom RMS fit for the two chains : 0.785
CA-only RMS fit for the two chains : 0.178

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: C and F

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.

1107 GOL   ( 960-)  B  -
1108 GOL   ( 962-)  D  -
1109 GOL   ( 961-)  E  -

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: G

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 284 GLN   ( 110-)  B      CB
 284 GLN   ( 110-)  B      CG
 284 GLN   ( 110-)  B      CD
 284 GLN   ( 110-)  B      OE1
 284 GLN   ( 110-)  B      NE2
 285 HIS   ( 111-)  B      CB
 285 HIS   ( 111-)  B      CG
 285 HIS   ( 111-)  B      ND1
 285 HIS   ( 111-)  B      CD2
 285 HIS   ( 111-)  B      CE1
 285 HIS   ( 111-)  B      NE2
 286 HIS   ( 112-)  B      CB
 286 HIS   ( 112-)  B      CG
 286 HIS   ( 112-)  B      ND1
 286 HIS   ( 112-)  B      CD2
 286 HIS   ( 112-)  B      CE1
 286 HIS   ( 112-)  B      NE2
 480 ASN   ( 103-)  G      CG
 480 ASN   ( 103-)  G      OD1
 480 ASN   ( 103-)  G      ND2
 481 SER   ( 104-)  G      OG
 482 HIS   ( 107-)  G      CG
 482 HIS   ( 107-)  G      ND1
 482 HIS   ( 107-)  G      CD2
 482 HIS   ( 107-)  G      CE1
And so on for a total of 104 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

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: G

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

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.

  48 ARG   (  50-)  A
  98 ARG   ( 100-)  A
 218 ARG   (  39-)  B
 227 ARG   (  48-)  B
 250 ARG   (  71-)  B
 259 ARG   (  80-)  B
 273 ARG   (  94-)  B
 307 ARG   ( 133-)  B
 363 ARG   ( 189-)  B
 435 ARG   (  58-)  G
 603 ARG   (  50-)  D
 629 ARG   (  76-)  D
 653 ARG   ( 100-)  D
 693 ARG   ( 140-)  D
 738 ARG   (   4-)  E
 782 ARG   (  48-)  E
 789 ARG   (  55-)  E
 805 ARG   (  71-)  E
 814 ARG   (  80-)  E
 858 ARG   ( 130-)  E
 861 ARG   ( 133-)  E
 894 ARG   ( 166-)  E
 917 ARG   ( 189-)  E
 989 ARG   (  58-)  H

Warning: Tyrosine convention problem

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

  77 TYR   (  79-)  A
 211 TYR   (  32-)  B
 345 TYR   ( 171-)  B
 632 TYR   (  79-)  D
 766 TYR   (  32-)  E
 836 TYR   ( 102-)  E
 899 TYR   ( 171-)  E

Warning: Phenylalanine convention problem

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

  49 PHE   (  51-)  A
 192 PHE   (  13-)  B
 329 PHE   ( 155-)  B
 403 PHE   (  26-)  G
 420 PHE   (  43-)  G
 444 PHE   (  67-)  G
 604 PHE   (  51-)  D
 665 PHE   ( 112-)  D
 860 PHE   ( 132-)  E
 998 PHE   (  67-)  H

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.

 108 ASP   ( 110-)  A
 169 ASP   ( 171-)  A
 245 ASP   (  66-)  B
 255 ASP   (  76-)  B
 326 ASP   ( 152-)  B
 457 ASP   (  80-)  G
 528 ASP   ( 153-)  G
 548 ASP   ( 173-)  G
 582 ASP   (  29-)  D
 663 ASP   ( 110-)  D
 800 ASP   (  66-)  E
 810 ASP   (  76-)  E
 880 ASP   ( 152-)  E
 994 ASP   (  63-)  H
1081 ASP   ( 153-)  H
1101 ASP   ( 173-)  H

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.

  28 GLU   (  30-)  A
  53 GLU   (  55-)  A
  96 GLU   (  98-)  A
 139 GLU   ( 141-)  A
 177 GLU   ( 179-)  A
 193 GLU   (  14-)  B
 215 GLU   (  36-)  B
 225 GLU   (  46-)  B
 231 GLU   (  52-)  B
 238 GLU   (  59-)  B
 248 GLU   (  69-)  B
 266 GLU   (  87-)  B
 302 GLU   ( 128-)  B
 361 GLU   ( 187-)  B
 454 GLU   (  77-)  G
 462 GLU   (  85-)  G
 464 GLU   (  87-)  G
 494 GLU   ( 119-)  G
 556 GLU   (   3-)  D
 574 GLU   (  21-)  D
 583 GLU   (  30-)  D
 651 GLU   (  98-)  D
 711 GLU   ( 158-)  D
 725 GLU   ( 172-)  D
 748 GLU   (  14-)  E
 769 GLU   (  35-)  E
 770 GLU   (  36-)  E
 780 GLU   (  46-)  E
 786 GLU   (  52-)  E
 803 GLU   (  69-)  E
 821 GLU   (  87-)  E
 890 GLU   ( 162-)  E
 897 GLU   ( 169-)  E
 944 GLU   (  13-)  H
1018 GLU   (  87-)  H

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

 |  0.999021  0.000145 -0.000019|
 |  0.000145  0.999100 -0.000160|
 | -0.000019 -0.000160  0.998572|
Proposed new scale matrix

 |  0.014883 -0.000001  0.004451|
 | -0.000001  0.007291  0.000001|
 |  0.000000  0.000002  0.011838|
With corresponding cell

    A    =  67.193  B   = 137.164  C    =  88.171
    Alpha=  90.022  Beta= 106.650  Gamma=  89.983

The CRYST1 cell dimensions

    A    =  67.260  B   = 137.290  C    =  88.290
    Alpha=  90.000  Beta= 106.640  Gamma=  90.000

Variance: 46.441
(Under-)estimated Z-score: 5.022

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.

   7 GLN   (   9-)  A      N    CA   C    99.38   -4.2
 161 CYS   ( 163-)  A      N    CA   C    98.29   -4.6
 417 TYR   (  40-)  G      N    CA   C    98.84   -4.4
 716 CYS   ( 163-)  D      N    CA   C    99.37   -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.

  28 GLU   (  30-)  A
  48 ARG   (  50-)  A
  53 GLU   (  55-)  A
  96 GLU   (  98-)  A
  98 ARG   ( 100-)  A
 108 ASP   ( 110-)  A
 139 GLU   ( 141-)  A
 169 ASP   ( 171-)  A
 177 GLU   ( 179-)  A
 193 GLU   (  14-)  B
 215 GLU   (  36-)  B
 218 ARG   (  39-)  B
 225 GLU   (  46-)  B
 227 ARG   (  48-)  B
 231 GLU   (  52-)  B
 238 GLU   (  59-)  B
 245 ASP   (  66-)  B
 248 GLU   (  69-)  B
 250 ARG   (  71-)  B
 255 ASP   (  76-)  B
 259 ARG   (  80-)  B
 266 GLU   (  87-)  B
 273 ARG   (  94-)  B
 302 GLU   ( 128-)  B
 307 ARG   ( 133-)  B
And so on for a total of 75 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.

 161 CYS   ( 163-)  A    4.76
 417 TYR   (  40-)  G    4.71
 109 LYS   ( 111-)  A    4.52
 716 CYS   ( 163-)  D    4.31
   7 GLN   (   9-)  A    4.06
 697 LEU   ( 144-)  D    4.06

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 666 THR   ( 113-)  D    -2.7
 127 THR   ( 129-)  A    -2.6
 828 ARG   (  94-)  E    -2.6
 100 PRO   ( 102-)  A    -2.5
 111 THR   ( 113-)  A    -2.5
1071 THR   ( 143-)  H    -2.5
 891 THR   ( 163-)  E    -2.5
 363 ARG   ( 189-)  B    -2.4
 882 THR   ( 154-)  E    -2.4
 435 ARG   (  58-)  G    -2.4
 328 THR   ( 154-)  B    -2.3
 523 GLN   ( 148-)  G    -2.3
 115 VAL   ( 117-)  A    -2.3
  88 THR   (  90-)  A    -2.3
 337 THR   ( 163-)  B    -2.3
 533 THR   ( 158-)  G    -2.3
 332 LEU   ( 158-)  B    -2.3
 886 LEU   ( 158-)  E    -2.3
 772 VAL   (  38-)  E    -2.2
 687 GLU   ( 134-)  D    -2.2
 670 VAL   ( 117-)  D    -2.2
 517 LYS   ( 142-)  G    -2.2
 491 LEU   ( 116-)  G    -2.2
 404 HIS   (  27-)  G    -2.2
 769 GLU   (  35-)  E    -2.2
And so on for a total of 51 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.

  13 ASN   (  15-)  A  PRO omega poor
  16 GLN   (  18-)  A  Poor phi/psi
  76 ASN   (  78-)  A  Poor phi/psi
  77 TYR   (  79-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 113 PRO   ( 115-)  A  Poor phi/psi
 123 GLY   ( 125-)  A  Poor phi/psi
 127 THR   ( 129-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 181 ASP   (   2-)  B  Poor phi/psi
 198 ASN   (  19-)  B  Poor phi/psi
 212 ASN   (  33-)  B  Poor phi/psi
 258 CYS   (  79-)  B  Poor phi/psi
 269 THR   (  90-)  B  Poor phi/psi
 285 HIS   ( 111-)  B  Poor phi/psi
 297 TYR   ( 123-)  B  PRO omega poor
 308 ASN   ( 134-)  B  Poor phi/psi
 327 TRP   ( 153-)  B  Poor phi/psi
 396 SER   (  19-)  G  Poor phi/psi
 410 GLN   (  33-)  G  Poor phi/psi
 429 ASN   (  52-)  G  Poor phi/psi
 457 ASP   (  80-)  G  Poor phi/psi
 464 GLU   (  87-)  G  Poor phi/psi
 465 ASP   (  88-)  G  Poor phi/psi
 523 GLN   ( 148-)  G  Poor phi/psi
And so on for a total of 58 lines.

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!

   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  15 ASP   (  17-)  A      0
  16 GLN   (  18-)  A      0
  24 PHE   (  26-)  A      0
  29 ILE   (  31-)  A      0
  30 PHE   (  32-)  A      0
  31 HIS   (  33-)  A      0
  42 ARG   (  44-)  A      0
  49 PHE   (  51-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 100 PRO   ( 102-)  A      0
 101 ASN   ( 103-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 110 PHE   ( 112-)  A      0
 111 THR   ( 113-)  A      0
 112 PRO   ( 114-)  A      0
 113 PRO   ( 115-)  A      0
 114 VAL   ( 116-)  A      0
 121 ARG   ( 123-)  A      0
And so on for a total of 451 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.378

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!

 299 GLY   ( 125-)  B   1.81   52
1051 GLY   ( 123-)  H   1.68   80
 853 GLY   ( 125-)  E   1.52   56

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 108 ASP   ( 110-)  A   1.66

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]

 137 PRO   ( 139-)  A    0.46 HIGH
 298 PRO   ( 124-)  B    0.46 HIGH
 852 PRO   ( 124-)  E    0.47 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  94 PRO   (  96-)  A  -114.5 envelop C-gamma (-108 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.

 145 LYS   ( 147-)  A      NZ  <->  147 HIS   ( 149-)  A      CE1    0.34    2.76  INTRA BL
 923 LYS   (   7-)  F      NZ  <->  925 ASN   (   9-)  F      OD1    0.31    2.39  INTRA BF
 932 LYS   (   1-)  H      CG  <->  933 LYS   (   2-)  H      N      0.30    2.70  INTRA BF
 856 GLU   ( 128-)  E      OE1 <->  858 ARG   ( 130-)  E      NH2    0.28    2.42  INTRA BL
1044 LEU   ( 116-)  H      CD1 <-> 1058 CYS   ( 130-)  H      SG     0.28    3.12  INTRA BF
1011 ASP   (  80-)  H      CG  <-> 1012 THR   (  81-)  H      N      0.28    2.72  INTRA BF
  74 ARG   (  76-)  A      NH1 <->  232 LEU   (  53-)  B      O      0.27    2.43  INTRA BL
 950 SER   (  19-)  H      N   <-> 1018 GLU   (  87-)  H      OE2    0.26    2.44  INTRA BF
 287 ASN   ( 113-)  B      ND2 <->  339 PRO   ( 165-)  B      CG     0.26    2.84  INTRA BF
 838 SER   ( 104-)  E      OG  <->  839 LYS   ( 105-)  E      N      0.25    2.35  INTRA BF
 193 GLU   (  14-)  B      OE2 <->  208 ARG   (  29-)  B      NH1    0.25    2.45  INTRA BL
 396 SER   (  19-)  G      N   <->  464 GLU   (  87-)  G      OE2    0.25    2.45  INTRA BF
 419 SER   (  42-)  G      O   <->  436 ARG   (  59-)  G      NH2    0.25    2.45  INTRA BF
 220 ASP   (  41-)  B      O   <->  223 VAL   (  44-)  B      N      0.24    2.46  INTRA BL
1060 SER   ( 132-)  H      O   <-> 1062 ARG   ( 134-)  H      N      0.23    2.47  INTRA BF
  74 ARG   (  76-)  A      NH1 <->  236 ASP   (  57-)  B      OD2    0.23    2.47  INTRA BL
 503 VAL   ( 128-)  G      CG1 <->  504 GLN   ( 129-)  G      N      0.23    2.77  INTRA BF
 742 LEU   (   8-)  E      O   <->  767 ASN   (  33-)  E      N      0.23    2.47  INTRA BL
 693 ARG   ( 140-)  D      NH2 <->  695 ASP   ( 142-)  D      OD2    0.22    2.48  INTRA BL
1060 SER   ( 132-)  H      C   <-> 1062 ARG   ( 134-)  H      N      0.21    2.69  INTRA BF
1033 ALA   ( 102-)  H      CB  <-> 1044 LEU   ( 116-)  H      CD2    0.20    3.00  INTRA BF
  26 GLY   (  28-)  A      O   <->  144 ARG   ( 146-)  A      NH2    0.19    2.51  INTRA BL
 462 GLU   (  85-)  G      OE2 <->  467 LYS   (  90-)  G      NZ     0.19    2.51  INTRA BF
 721 TRP   ( 168-)  D      CH2 <->  740 ARG   (   6-)  E      CZ     0.19    3.01  INTRA BL
 369 LYS   (   7-)  C      CE  <->  371 ASN   (   9-)  C      ND2    0.18    2.92  INTRA BF
And so on for a total of 168 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: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

 509 ARG   ( 134-)  G      -7.72
1062 ARG   ( 134-)  H      -7.62
  98 ARG   ( 100-)  A      -7.19
 653 ARG   ( 100-)  D      -6.99
 917 ARG   ( 189-)  E      -6.34
 894 ARG   ( 166-)  E      -6.17
 363 ARG   ( 189-)  B      -5.54
1038 GLN   ( 110-)  H      -5.43
 273 ARG   (  94-)  B      -5.40
 571 GLN   (  18-)  D      -5.38
  16 GLN   (  18-)  A      -5.25
 603 ARG   (  50-)  D      -5.16
 441 GLN   (  64-)  G      -5.13
  48 ARG   (  50-)  A      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

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: G

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

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: E

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: F

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: H

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.

1079 LEU   ( 151-)  H   -3.36
1076 GLN   ( 148-)  H   -3.24
 286 HIS   ( 112-)  B   -3.16
1077 LEU   ( 149-)  H   -3.01
1035 HIS   ( 107-)  H   -3.00
1064 LYS   ( 136-)  H   -2.97
 511 LYS   ( 136-)  G   -2.92
1078 GLU   ( 150-)  H   -2.79
 526 LEU   ( 151-)  G   -2.70
 285 HIS   ( 111-)  B   -2.66
 555 LYS   (   2-)  D   -2.62
 428 LEU   (  51-)  G   -2.60
 525 GLU   ( 150-)  G   -2.59
 982 LEU   (  51-)  H   -2.59

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.

 283 SER   ( 104-)  B     -  286 HIS   ( 112-)  B        -1.50
1075 SER   ( 147-)  H     - 1079 LEU   ( 151-)  H        -2.77
1101 ASP   ( 173-)  H     - 1104 VAL   ( 176-)  H        -1.77

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: G

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

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.

1110 HOH   ( 184 )  A      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.

 141 HIS   ( 143-)  A
 147 HIS   ( 149-)  A
 249 GLN   (  70-)  B
 261 ASN   (  82-)  B
 310 GLN   ( 136-)  B
 324 ASN   ( 150-)  B
 370 GLN   (   8-)  C
 487 GLN   ( 112-)  G
 512 ASN   ( 137-)  G
 586 HIS   (  33-)  D
 696 HIS   ( 143-)  D
 804 GLN   (  70-)  E
 816 ASN   (  82-)  E
 862 ASN   ( 134-)  E
 864 GLN   ( 136-)  E
 877 GLN   ( 149-)  E
 956 GLN   (  25-)  H
 963 ASN   (  32-)  H
 997 ASN   (  66-)  H
1020 GLN   (  89-)  H
1065 ASN   ( 137-)  H
1080 GLN   ( 152-)  H
1092 ASN   ( 164-)  H

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.

  43 LEU   (  45-)  A      N
  55 GLN   (  57-)  A      N
  65 LYS   (  67-)  A      NZ
  96 GLU   (  98-)  A      N
  99 GLU   ( 101-)  A      N
 101 ASN   ( 103-)  A      ND2
 111 THR   ( 113-)  A      OG1
 116 ASN   ( 118-)  A      ND2
 119 TRP   ( 121-)  A      NE1
 166 TRP   ( 168-)  A      N
 208 ARG   (  29-)  B      NE
 225 GLU   (  46-)  B      N
 254 VAL   (  75-)  B      N
 261 ASN   (  82-)  B      ND2
 304 ARG   ( 130-)  B      NH1
 307 ARG   ( 133-)  B      NE
 309 GLY   ( 135-)  B      N
 356 SER   ( 182-)  B      N
 370 GLN   (   8-)  C      NE2
 398 LYS   (  21-)  G      N
 401 ILE   (  24-)  G      N
 404 HIS   (  27-)  G      NE2
 432 ALA   (  55-)  G      N
 454 GLU   (  77-)  G      N
 469 GLU   (  92-)  G      N
And so on for a total of 66 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.

   1 GLU   (   3-)  A      OE2
  64 ASP   (  66-)  A      OD1
  64 ASP   (  66-)  A      OD2
 619 ASP   (  66-)  D      OD2
 702 HIS   ( 149-)  D      ND1
1081 ASP   ( 153-)  H      OD1

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.

   1 GLU   (   3-)  A   H-bonding suggests Gln
  19 GLU   (  21-)  A   H-bonding suggests Gln
  64 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
 156 GLU   ( 158-)  A   H-bonding suggests Gln
 157 ASP   ( 159-)  A   H-bonding suggests Asn; but Alt-Rotamer
 245 ASP   (  66-)  B   H-bonding suggests Asn
 433 ASP   (  56-)  G   H-bonding suggests Asn; but Alt-Rotamer
 468 GLU   (  91-)  G   H-bonding suggests Gln; but Alt-Rotamer
 556 GLU   (   3-)  D   H-bonding suggests Gln
 574 GLU   (  21-)  D   H-bonding suggests Gln
 619 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer
 715 ASP   ( 162-)  D   H-bonding suggests Asn; but Alt-Rotamer
 793 GLU   (  59-)  E   H-bonding suggests Gln
1011 ASP   (  80-)  H   H-bonding suggests Asn
1022 GLU   (  91-)  H   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 :  -0.083
  2nd generation packing quality :  -1.405
  Ramachandran plot appearance   :  -2.012
  chi-1/chi-2 rotamer normality  :  -2.812
  Backbone conformation          :   0.235

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.338 (tight)
  Bond angles                    :   0.641 (tight)
  Omega angle restraints         :   0.250 (tight)
  Side chain planarity           :   0.234 (tight)
  Improper dihedral distribution :   0.631
  B-factor distribution          :   0.485
  Inside/Outside distribution    :   1.012

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 :   0.8
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.338 (tight)
  Bond angles                    :   0.641 (tight)
  Omega angle restraints         :   0.250 (tight)
  Side chain planarity           :   0.234 (tight)
  Improper dihedral distribution :   0.631
  B-factor distribution          :   0.485
  Inside/Outside distribution    :   1.012
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
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      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
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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Checking checks
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      Who checks the checkers
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