WHAT IF Check report

This file was created 2013-12-10 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 pdb4bnt.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 : 1.862
CA-only RMS fit for the two chains : 1.491

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

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.

 951 36E   (1248-)  B  -
 952 36E   (1248-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 PHE   (  -2-)  A    High
  77 GLU   (  74-)  A    High
  78 HIS   (  75-)  A    High
  95 LYS   ( 102-)  A    High
  98 GLU   ( 105-)  A    High
 239 MET   ( 246-)  A    High
 320 HIS   (  79-)  B    High
 371 ASN   ( 148-)  B    High
 372 ALA   ( 149-)  B    High
 374 GLN   ( 151-)  B    High
 606 ASN   ( 148-)  C    High
 648 ASP   ( 190-)  C    High
 649 MET   ( 191-)  C    High
 801 MET   ( 101-)  D    High
 826 ARG   ( 126-)  D    High
 846 MET   ( 146-)  D    High
 889 THR   ( 189-)  D    High
 890 ASP   ( 190-)  D    High
 891 MET   ( 191-)  D    High
 894 GLU   ( 194-)  D    High
 895 LEU   ( 195-)  D    High
 896 PRO   ( 196-)  D    High
 897 GLU   ( 197-)  D    High
 898 ALA   ( 198-)  D    High
 900 ARG   ( 200-)  D    High
 946 MET   ( 246-)  D    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 4

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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

 |  0.999238  0.000321 -0.000265|
 |  0.000321  1.000221  0.000424|
 | -0.000265  0.000424  0.998138|
Proposed new scale matrix

 |  0.018471 -0.000006  0.000005|
 | -0.000003  0.009160 -0.000004|
 |  0.000002 -0.000003  0.006900|
With corresponding cell

    A    =  54.139  B   = 109.171  C    = 144.931
    Alpha=  89.951  Beta=  90.030  Gamma=  89.963

The CRYST1 cell dimensions

    A    =  54.180  B   = 109.152  C    = 145.194
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 29.035
(Under-)estimated Z-score: 3.971

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.

 268 ARG   (  27-)  B      CD   NE   CZ  128.90    4.0
 316 HIS   (  75-)  B      CG   ND1  CE1 109.66    4.1
 319 GLN   (  78-)  B      CA   CB   CG  122.59    4.2
 476 MET   (   1-)  C      CA   CB   CG  105.73   -4.2

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.

 300 LEU   (  59-)  B    -2.4
  62 LEU   (  59-)  A    -2.4
 179 PHE   ( 186-)  A    -2.3
 457 THR   ( 234-)  B    -2.3
 227 THR   ( 234-)  A    -2.3
 692 THR   ( 234-)  C    -2.3
 225 TYR   ( 232-)  A    -2.3
 934 THR   ( 234-)  D    -2.2
 409 PHE   ( 186-)  B    -2.2
 455 TYR   ( 232-)  B    -2.1
 242 MET   (   1-)  B    -2.1

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.

  33 ALA   (  30-)  A  omega poor
  83 LEU   (  80-)  A  Poor phi/psi
 136 VAL   ( 143-)  A  omega poor
 169 ALA   ( 176-)  A  Poor phi/psi
 233 VAL   ( 240-)  A  omega poor
 271 ALA   (  30-)  B  omega poor
 321 LEU   (  80-)  B  Poor phi/psi
 359 ARG   ( 132-)  B  Poor phi/psi
 399 ALA   ( 176-)  B  Poor phi/psi
 463 VAL   ( 240-)  B  omega poor
 476 MET   (   1-)  C  omega poor
 480 GLY   (   5-)  C  Poor phi/psi
 505 ALA   (  30-)  C  omega poor
 555 LEU   (  80-)  C  Poor phi/psi
 634 ALA   ( 176-)  C  Poor phi/psi
 698 VAL   ( 240-)  C  omega poor
 704 MET   ( 246-)  C  omega poor
 711 MET   (   1-)  D  Poor phi/psi
 740 ALA   (  30-)  D  omega poor
 790 LEU   (  80-)  D  Poor phi/psi
 843 VAL   ( 143-)  D  omega poor
 844 GLY   ( 144-)  D  omega poor
 845 ALA   ( 145-)  D  Poor phi/psi, omega poor
 876 ALA   ( 176-)  D  Poor phi/psi
 940 VAL   ( 240-)  D  omega poor
 chi-1/chi-2 correlation Z-score : -1.396

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.

 816 SER   ( 116-)  D    0.39

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!

   6 LEU   (   3-)  A      0
   7 GLN   (   4-)  A      0
  14 THR   (  11-)  A      0
  16 ALA   (  13-)  A      0
  17 SER   (  14-)  A      0
  20 ILE   (  17-)  A      0
  31 LEU   (  28-)  A      0
  58 GLU   (  55-)  A      0
  60 ALA   (  57-)  A      0
  83 LEU   (  80-)  A      0
  86 PRO   (  83-)  A      0
  87 LEU   (  84-)  A      0
  92 ASN   (  89-)  A      0
  93 ALA   (  90-)  A      0
  94 MET   ( 101-)  A      0
  95 LYS   ( 102-)  A      0
  98 GLU   ( 105-)  A      0
 125 ARG   ( 132-)  A      0
 126 TRP   ( 133-)  A      0
 136 VAL   ( 143-)  A      0
 139 MET   ( 146-)  A      0
 169 ALA   ( 176-)  A      0
 179 PHE   ( 186-)  A      0
 226 VAL   ( 233-)  A      0
 227 THR   ( 234-)  A      0
And so on for a total of 242 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!

 844 GLY   ( 144-)  D   2.66   14

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]

 189 PRO   ( 196-)  A    0.14 LOW
 232 PRO   ( 239-)  A    0.16 LOW
 419 PRO   ( 196-)  B    0.12 LOW
 462 PRO   ( 239-)  B    0.12 LOW
 654 PRO   ( 196-)  C    0.04 LOW
 697 PRO   ( 239-)  C    0.14 LOW
 896 PRO   ( 196-)  D    0.13 LOW
 939 PRO   ( 239-)  D    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].

 177 PRO   ( 184-)  A    39.0 envelop C-delta (36 degrees)
 324 PRO   (  83-)  B   -65.6 envelop C-beta (-72 degrees)
 407 PRO   ( 184-)  B    41.8 envelop C-delta (36 degrees)
 642 PRO   ( 184-)  C    44.7 envelop C-delta (36 degrees)
 666 PRO   ( 208-)  C   100.0 envelop C-beta (108 degrees)
 884 PRO   ( 184-)  D    38.0 envelop C-delta (36 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.

 725 ARG   (  15-)  D      NH1 <->  956 HOH   (2005 )  D      O      0.43    2.27  INTRA BF
 886 PHE   ( 186-)  D      CE2 <->  944 MET   ( 244-)  D      SD     0.34    3.06  INTRA BF
 569 PHE   ( 107-)  C      CE1 <->  952 36E   (1248-)  C      FAC    0.34    2.86  INTRA BL
 644 PHE   ( 186-)  C      CE2 <->  702 MET   ( 244-)  C      SD     0.34    3.06  INTRA BF
 573 ASN   ( 111-)  C      N   <->  952 36E   (1248-)  C      FAH    0.33    2.77  INTRA BL
  22 GLN   (  19-)  A      NE2 <->   47 LYS   (  44-)  A      NZ     0.28    2.57  INTRA BF
 568 TRP   ( 106-)  C      NE1 <->  871 GLU   ( 171-)  D      OE1    0.27    2.43  INTRA BF
 164 GLU   ( 171-)  A      OE1 <->  333 TRP   ( 106-)  B      NE1    0.25    2.45  INTRA BF
  99 TRP   ( 106-)  A      NE1 <->  394 GLU   ( 171-)  B      OE1    0.20    2.50  INTRA
 572 VAL   ( 110-)  C      CG1 <->  952 36E   (1248-)  C      FAH    0.19    3.01  INTRA BL
 137 GLY   ( 144-)  A      O   <->  192 GLN   ( 199-)  A      NE2    0.19    2.51  INTRA BF
  94 MET   ( 101-)  A      CE  <->  138 ALA   ( 145-)  A      CB     0.16    3.04  INTRA BF
 827 GLY   ( 127-)  D      N   <->  956 HOH   (2016 )  D      O      0.16    2.54  INTRA
 816 SER   ( 116-)  D      CB  <->  956 HOH   (2014 )  D      O      0.15    2.65  INTRA
 649 MET   ( 191-)  C      N   <->  955 HOH   (2023 )  C      O      0.14    2.56  INTRA BF
 709 GLN   (  -1-)  D      NE2 <->  956 HOH   (2001 )  D      O      0.12    2.58  INTRA BF
 858 LYS   ( 158-)  D      NZ  <->  946 MET   ( 246-)  D      O      0.11    2.59  INTRA BF
  27 GLU   (  24-)  A      OE2 <->   30 ARG   (  27-)  A      NH2    0.10    2.60  INTRA BF
 136 VAL   ( 143-)  A      CG1 <->  179 PHE   ( 186-)  A      CA     0.09    3.11  INTRA
 886 PHE   ( 186-)  D      CZ  <->  903 LEU   ( 203-)  D      CD1    0.08    3.12  INTRA BF
 572 VAL   ( 110-)  C      CB  <->  952 36E   (1248-)  C      FAH    0.08    3.12  INTRA BL
 338 ASN   ( 111-)  B      O   <->  342 ASN   ( 115-)  B      ND2    0.07    2.63  INTRA BF
 464 ASN   ( 241-)  B      ND2 <->  954 HOH   (2013 )  B      O      0.07    2.63  INTRA BL
 644 PHE   ( 186-)  C      CD2 <->  702 MET   ( 244-)  C      SD     0.07    3.33  INTRA BF
 104 ASN   ( 111-)  A      ND2 <->  338 ASN   ( 111-)  B      OD1    0.07    2.63  INTRA BF
 104 ASN   ( 111-)  A      O   <->  108 ASN   ( 115-)  A      ND2    0.06    2.64  INTRA
 573 ASN   ( 111-)  C      O   <->  577 ASN   ( 115-)  C      ND2    0.06    2.64  INTRA BL
  94 MET   ( 101-)  A      CE  <->  143 GLY   ( 150-)  A      CA     0.05    3.15  INTRA BF
 126 TRP   ( 133-)  A      NE1 <->  953 HOH   (2014 )  A      O      0.05    2.65  INTRA BL
 584 LYS   ( 122-)  C      NZ  <->  629 GLU   ( 171-)  C      OE2    0.04    2.66  INTRA BL
 428 GLY   ( 205-)  B      O   <->  848 ASN   ( 148-)  D      ND2    0.04    2.66  INTRA BF
 811 ASN   ( 111-)  D      O   <->  815 ASN   ( 115-)  D      ND2    0.04    2.66  INTRA BL
 307 ASP   (  66-)  B      OD1 <->  346 ARG   ( 119-)  B      NE     0.03    2.67  INTRA BF
 907 ILE   ( 207-)  D      O   <->  910 GLY   ( 210-)  D      N      0.03    2.67  INTRA BL
 886 PHE   ( 186-)  D      CD2 <->  944 MET   ( 244-)  D      SD     0.03    3.37  INTRA BF
 724 SER   (  14-)  D      O   <->  754 LYS   (  44-)  D      NZ     0.03    2.67  INTRA BF
 803 ASP   ( 103-)  D      O   <->  806 TRP   ( 106-)  D      CD1    0.03    2.77  INTRA
 362 ARG   ( 135-)  B      NH2 <->  954 HOH   (2008 )  B      O      0.02    2.68  INTRA BL
 136 VAL   ( 143-)  A      CG2 <->  137 GLY   ( 144-)  A      N      0.02    2.98  INTRA BF
  69 ASP   (  66-)  A      OD1 <->  112 ARG   ( 119-)  A      NE     0.02    2.68  INTRA BF
 300 LEU   (  59-)  B      CD1 <->  313 THR   (  72-)  B      CG2    0.01    3.19  INTRA BF
 776 ASP   (  66-)  D      OD1 <->  819 ARG   ( 119-)  D      NE     0.01    2.69  INTRA BF
 475 SER   (   0-)  C      N   <->  476 MET   (   1-)  C      N      0.01    2.59  INTRA BF
 665 ILE   ( 207-)  C      O   <->  668 GLY   ( 210-)  C      N      0.01    2.69  INTRA BL
 541 ASP   (  66-)  C      OD1 <->  581 ARG   ( 119-)  C      NE     0.01    2.69  INTRA BF

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

 139 MET   ( 146-)  A      -7.48
 239 MET   ( 246-)  A      -7.10
 725 ARG   (  15-)  D      -6.88
 490 ARG   (  15-)  C      -6.72
 789 HIS   (  79-)  D      -6.45
 472 TYR   (  -3-)  C      -6.43
 554 HIS   (  79-)  C      -6.42
  82 HIS   (  79-)  A      -6.40
 320 HIS   (  79-)  B      -6.28
 256 ARG   (  15-)  B      -6.09
  18 ARG   (  15-)  A      -6.05
 469 MET   ( 246-)  B      -5.96
 711 MET   (   1-)  D      -5.87
 846 MET   ( 146-)  D      -5.71
 204 ARG   ( 211-)  A      -5.69
 911 ARG   ( 211-)  D      -5.65
 268 ARG   (  27-)  B      -5.60
 669 ARG   ( 211-)  C      -5.57
 434 ARG   ( 211-)  B      -5.54
 502 ARG   (  27-)  C      -5.48
  30 ARG   (  27-)  A      -5.47
 737 ARG   (  27-)  D      -5.42
 946 MET   ( 246-)  D      -5.38
 242 MET   (   1-)  B      -5.38
 474 GLN   (  -1-)  C      -5.30
 708 PHE   (  -2-)  D      -5.28
 707 TYR   (  -3-)  D      -5.25
 319 GLN   (  78-)  B      -5.23
 704 MET   ( 246-)  C      -5.11
  81 GLN   (  78-)  A      -5.08
 875 ARG   ( 175-)  D      -5.06
 398 ARG   ( 175-)  B      -5.03
 633 ARG   ( 175-)  C      -5.02

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 472 TYR   (  -3-)  C       474 - GLN     -1- ( C)         -5.34

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 207 GLN   ( 214-)  A
 376 ASN   ( 153-)  B
 429 GLN   ( 206-)  B
 557 GLN   (  82-)  C
 609 GLN   ( 151-)  C
 853 ASN   ( 153-)  D
 906 GLN   ( 206-)  D
 914 GLN   ( 214-)  D

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  18 ARG   (  15-)  A      N
  91 ASN   (  88-)  A      ND2
 100 PHE   ( 107-)  A      N
 101 ASP   ( 108-)  A      N
 104 ASN   ( 111-)  A      ND2
 131 ASN   ( 138-)  A      ND2
 170 ILE   ( 177-)  A      N
 180 ILE   ( 187-)  A      N
 193 ARG   ( 200-)  A      NH1
 204 ARG   ( 211-)  A      N
 256 ARG   (  15-)  B      N
 259 GLY   (  18-)  B      N
 334 PHE   ( 107-)  B      N
 335 ASP   ( 108-)  B      N
 400 ILE   ( 177-)  B      N
 410 ILE   ( 187-)  B      N
 434 ARG   ( 211-)  B      N
 438 ALA   ( 215-)  B      N
 476 MET   (   1-)  C      N
 490 ARG   (  15-)  C      N
 493 GLY   (  18-)  C      N
 513 SER   (  38-)  C      N
 567 GLU   ( 105-)  C      N
 568 TRP   ( 106-)  C      N
 569 PHE   ( 107-)  C      N
 597 ARG   ( 135-)  C      NH2
 600 ASN   ( 138-)  C      ND2
 635 ILE   ( 177-)  C      N
 669 ARG   ( 211-)  C      N
 673 ALA   ( 215-)  C      N
 707 TYR   (  -3-)  D      OH
 711 MET   (   1-)  D      N
 798 ASN   (  88-)  D      ND2
 802 LYS   ( 102-)  D      N
 804 ASP   ( 104-)  D      N
 806 TRP   ( 106-)  D      N
 877 ILE   ( 177-)  D      N
 887 ILE   ( 187-)  D      N
 889 THR   ( 189-)  D      OG1
 890 ASP   ( 190-)  D      N
 911 ARG   ( 211-)  D      N

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.

 320 HIS   (  79-)  B      ND1
 714 GLN   (   4-)  D      OE1

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 :   0.562
  2nd generation packing quality :   0.195
  Ramachandran plot appearance   :   0.286
  chi-1/chi-2 rotamer normality  :  -1.396
  Backbone conformation          :   1.722

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.667
  Bond angles                    :   0.768
  Omega angle restraints         :   0.948
  Side chain planarity           :   0.942
  Improper dihedral distribution :   0.974
  B-factor distribution          :   0.745
  Inside/Outside distribution    :   0.953

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.4
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   1.4
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :   1.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.667
  Bond angles                    :   0.768
  Omega angle restraints         :   0.948
  Side chain planarity           :   0.942
  Improper dihedral distribution :   0.974
  B-factor distribution          :   0.745
  Inside/Outside distribution    :   0.953
==============

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.