WHAT IF Check report

This file was created 2011-12-15 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 pdb3e3g.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 : 0.953
CA-only RMS fit for the two chains : 0.615

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

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 D

All-atom RMS fit for the two chains : 0.820
CA-only RMS fit for the two chains : 0.542

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 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: E and F

All-atom RMS fit for the two chains : 0.955
CA-only RMS fit for the two chains : 0.450

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: E and F

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1241 SO4   ( 231-)  D  C

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.

1233 SO4   ( 231-)  A  -
1234 SO4   ( 232-)  A  -
1235 SO4   ( 233-)  A  -
1237 SO4   ( 234-)  A  -
1238 SO4   ( 231-)  B  -
1240 SO4   ( 232-)  B  -
1241 SO4   ( 231-)  D  C
1243 SO4   ( 232-)  C  -
1245 SO4   ( 231-)  D  -
1246 SO4   ( 231-)  E  -
1247 SO4   ( 232-)  E  -
1249 SO4   ( 233-)  E  -
1250 SO4   ( 231-)  F  -

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

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: 6

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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

 167 TYR   ( 181-)  A
 230 TYR   (  37-)  B
 426 TYR   (  12-)  C
 436 TYR   (  37-)  C
 630 TYR   (  12-)  D
 640 TYR   (  37-)  D
 784 TYR   ( 181-)  D
 830 TYR   (  12-)  E
1049 TYR   (  37-)  F

Warning: Phenylalanine convention problem

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

  61 PHE   (  75-)  A
 173 PHE   ( 187-)  A
 268 PHE   (  75-)  B
 380 PHE   ( 187-)  B
 474 PHE   (  75-)  C
 527 PHE   ( 128-)  C
 586 PHE   ( 187-)  C
 678 PHE   (  75-)  D
 731 PHE   ( 128-)  D
 790 PHE   ( 187-)  D
 880 PHE   (  75-)  E
 992 PHE   ( 187-)  E
1087 PHE   (  75-)  F
1199 PHE   ( 187-)  F

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.

  30 ASP   (  44-)  A
  96 ASP   ( 110-)  A
 130 ASP   ( 144-)  A
 209 ASP   (   2-)  B
 337 ASP   ( 144-)  B
 409 ASP   ( 216-)  B
 543 ASP   ( 144-)  C
 584 ASP   ( 185-)  C
 713 ASP   ( 110-)  D
 747 ASP   ( 144-)  D
 788 ASP   ( 185-)  D
 820 ASP   (   2-)  E
 949 ASP   ( 144-)  E
 990 ASP   ( 185-)  E
1027 ASP   (   2-)  F
1156 ASP   ( 144-)  F

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.

  36 GLU   (  50-)  A
  77 GLU   (  91-)  A
 155 GLU   ( 169-)  A
 204 GLU   ( 218-)  A
 249 GLU   (  56-)  B
 252 GLU   (  59-)  B
 284 GLU   (  91-)  B
 392 GLU   ( 199-)  B
 410 GLU   ( 217-)  B
 458 GLU   (  59-)  C
 598 GLU   ( 199-)  C
 616 GLU   ( 217-)  C
 659 GLU   (  56-)  D
 662 GLU   (  59-)  D
 694 GLU   (  91-)  D
 772 GLU   ( 169-)  D
 861 GLU   (  56-)  E
 896 GLU   (  91-)  E
1004 GLU   ( 199-)  E
1007 GLU   ( 202-)  E
1022 GLU   ( 217-)  E
1023 GLU   ( 218-)  E
1068 GLU   (  56-)  F
1103 GLU   (  91-)  F
1152 GLU   ( 140-)  F
1229 GLU   ( 217-)  F
1230 GLU   ( 218-)  F

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

 |  0.997980  0.000057  0.000056|
 |  0.000057  0.997759 -0.000128|
 |  0.000056 -0.000128  0.997870|
Proposed new scale matrix

 |  0.004321  0.000000  0.000288|
 |  0.000000  0.006901  0.000000|
 | -0.000001  0.000002  0.018960|
With corresponding cell

    A    = 231.442  B   = 144.897  C    =  52.859
    Alpha=  90.008  Beta=  93.815  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 231.925  B   = 145.231  C    =  52.972
    Alpha=  90.000  Beta=  93.820  Gamma=  90.000

Variance: 192.146
(Under-)estimated Z-score: 10.216

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.

 237 ASP   (  44-)  B      C    CA   CB   99.92   -5.4
 291 HIS   (  98-)  B      CG   ND1  CE1 109.66    4.1
 521 HIS   ( 122-)  C      CG   ND1  CE1 109.73    4.1
 647 ASP   (  44-)  D      C    CA   CB   95.83   -7.5
 927 HIS   ( 122-)  E      CG   ND1  CE1 109.69    4.1
1056 ASP   (  44-)  F      C    CA   CB  100.61   -5.0
1076 ARG   (  64-)  F      CG   CD   NE  118.67    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.

  30 ASP   (  44-)  A
  36 GLU   (  50-)  A
  77 GLU   (  91-)  A
  96 ASP   ( 110-)  A
 130 ASP   ( 144-)  A
 155 GLU   ( 169-)  A
 204 GLU   ( 218-)  A
 209 ASP   (   2-)  B
 249 GLU   (  56-)  B
 252 GLU   (  59-)  B
 284 GLU   (  91-)  B
 337 ASP   ( 144-)  B
 392 GLU   ( 199-)  B
 409 ASP   ( 216-)  B
 410 GLU   ( 217-)  B
 458 GLU   (  59-)  C
 543 ASP   ( 144-)  C
 584 ASP   ( 185-)  C
 598 GLU   ( 199-)  C
 616 GLU   ( 217-)  C
 659 GLU   (  56-)  D
 662 GLU   (  59-)  D
 694 GLU   (  91-)  D
 713 ASP   ( 110-)  D
 747 ASP   ( 144-)  D
 772 GLU   ( 169-)  D
 788 ASP   ( 185-)  D
 820 ASP   (   2-)  E
 861 GLU   (  56-)  E
 896 GLU   (  91-)  E
 949 ASP   ( 144-)  E
 990 ASP   ( 185-)  E
1004 GLU   ( 199-)  E
1007 GLU   ( 202-)  E
1022 GLU   ( 217-)  E
1023 GLU   ( 218-)  E
1027 ASP   (   2-)  F
1068 GLU   (  56-)  F
1103 GLU   (  91-)  F
1152 GLU   ( 140-)  F
1156 ASP   ( 144-)  F
1229 GLU   ( 217-)  F
1230 GLU   ( 218-)  F

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.

 102 ILE   ( 116-)  A    4.00

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.

 444 SER   (  45-)  C    -2.6
 102 ILE   ( 116-)  A    -2.3
 937 HIS   ( 132-)  E    -2.2
 467 ASN   (  68-)  C    -2.2
1149 LEU   ( 137-)  F    -2.2
1128 ILE   ( 116-)  F    -2.2
 164 GLY   ( 178-)  A    -2.2
 371 GLY   ( 178-)  B    -2.1
 309 ILE   ( 116-)  B    -2.1
 577 GLY   ( 178-)  C    -2.1
 983 GLY   ( 178-)  E    -2.1
1190 GLY   ( 178-)  F    -2.1
 781 GLY   ( 178-)  D    -2.1
 238 SER   (  45-)  B    -2.1
1057 SER   (  45-)  F    -2.1
 671 ASN   (  68-)  D    -2.1
1080 ASN   (  68-)  F    -2.1
 387 MET   ( 194-)  B    -2.1
 921 ILE   ( 116-)  E    -2.1
  54 ASN   (  68-)  A    -2.0
 895 ILE   (  90-)  E    -2.0
 125 PRO   ( 139-)  A    -2.0
  59 THR   (  73-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  23 TYR   (  37-)  A  omega poor
  47 PHE   (  61-)  A  omega poor
  53 ALA   (  67-)  A  Poor phi/psi
  55 GLN   (  69-)  A  omega poor
  75 LYS   (  89-)  A  Poor phi/psi
  86 ASN   ( 100-)  A  Poor phi/psi
 171 ASP   ( 185-)  A  Poor phi/psi
 254 PHE   (  61-)  B  omega poor
 260 ALA   (  67-)  B  Poor phi/psi
 262 GLN   (  69-)  B  omega poor
 282 LYS   (  89-)  B  Poor phi/psi
 390 SER   ( 197-)  B  Poor phi/psi
 410 GLU   ( 217-)  B  Poor phi/psi
 431 ARG   (  17-)  C  Poor phi/psi, omega poor
 436 TYR   (  37-)  C  omega poor
 443 ASP   (  44-)  C  omega poor
 444 SER   (  45-)  C  Poor phi/psi
 445 ARG   (  46-)  C  Poor phi/psi
 460 PHE   (  61-)  C  omega poor
 466 ALA   (  67-)  C  Poor phi/psi
 488 LYS   (  89-)  C  Poor phi/psi
 640 TYR   (  37-)  D  omega poor
 664 PHE   (  61-)  D  omega poor
 670 ALA   (  67-)  D  Poor phi/psi
 672 GLN   (  69-)  D  omega poor
 674 ILE   (  71-)  D  omega poor
 692 LYS   (  89-)  D  Poor phi/psi
 703 ASN   ( 100-)  D  Poor phi/psi
 820 ASP   (   2-)  E  Poor phi/psi
 849 ASP   (  44-)  E  omega poor
 850 SER   (  45-)  E  Poor phi/psi, omega poor
 866 PHE   (  61-)  E  omega poor
 872 ALA   (  67-)  E  Poor phi/psi
 874 GLN   (  69-)  E  omega poor
 876 ILE   (  71-)  E  omega poor
 894 LYS   (  89-)  E  Poor phi/psi
1002 SER   ( 197-)  E  Poor phi/psi
1024 ASN   ( 219-)  E  omega poor
1049 TYR   (  37-)  F  omega poor
1056 ASP   (  44-)  F  omega poor
1066 ASN   (  54-)  F  Poor phi/psi
1073 PHE   (  61-)  F  omega poor
1079 ALA   (  67-)  F  Poor phi/psi
1081 GLN   (  69-)  F  omega poor
1101 LYS   (  89-)  F  Poor phi/psi
1228 ASP   ( 216-)  F  omega poor
 chi-1/chi-2 correlation Z-score : -2.762

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!

  17 ARG   (  17-)  A      0
  18 MET   (  18-)  A      0
  19 GLN   (  33-)  A      0
  20 THR   (  34-)  A      0
  32 ARG   (  46-)  A      0
  43 PRO   (  57-)  A      0
  45 GLU   (  59-)  A      0
  51 ASN   (  65-)  A      0
  52 VAL   (  66-)  A      0
  53 ALA   (  67-)  A      0
  54 ASN   (  68-)  A      0
  55 GLN   (  69-)  A      0
  58 HIS   (  72-)  A      0
  59 THR   (  73-)  A      0
  72 ASP   (  86-)  A      0
  74 LEU   (  88-)  A      0
  75 LYS   (  89-)  A      0
  77 GLU   (  91-)  A      0
  85 THR   (  99-)  A      0
  87 CYS   ( 101-)  A      0
  96 ASP   ( 110-)  A      0
  99 LEU   ( 113-)  A      0
 101 LEU   ( 115-)  A      0
 159 LYS   ( 173-)  A      0
 177 GLN   ( 191-)  A      0
And so on for a total of 377 lines.

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].

  21 PRO   (  35-)  A   -63.1 envelop C-beta (-72 degrees)
 125 PRO   ( 139-)  A    99.1 envelop C-beta (108 degrees)
 228 PRO   (  35-)  B    37.0 envelop C-delta (36 degrees)
 434 PRO   (  35-)  C   -17.9 half-chair C-alpha/N (-18 degrees)
 456 PRO   (  57-)  C  -120.1 half-chair C-delta/C-gamma (-126 degrees)
 638 PRO   (  35-)  D   -57.5 half-chair C-beta/C-alpha (-54 degrees)
 862 PRO   (  57-)  E  -131.2 half-chair C-delta/C-gamma (-126 degrees)
 944 PRO   ( 139-)  E   110.5 envelop C-beta (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.

 262 GLN   (  69-)  B      NE2 <->  316 ILE   ( 123-)  B      CD1    0.54    2.56  INTRA BF
 239 ARG   (  46-)  B      N   <-> 1240 SO4   ( 232-)  B      O3     0.53    2.17  INTRA BF
 784 TYR   ( 181-)  D      OH  <-> 1245 SO4   ( 231-)  D      O2     0.45    1.95  INTRA BF
 819 MET   (   1-)  E      O   <->  822 ILE   (   4-)  E      N      0.43    2.27  INTRA BF
 784 TYR   ( 181-)  D      OH  <-> 1245 SO4   ( 231-)  D      S      0.41    2.59  INTRA BF
 167 TYR   ( 181-)  A      OH  <-> 1237 SO4   ( 234-)  A      O2     0.34    2.06  INTRA BL
 237 ASP   (  44-)  B      CB  <-> 1236  ZN   ( 230-)  B     ZN      0.33    2.87  INTRA BL
   1 MET   (   1-)  A      O   <->    5 LYS   (   5-)  A      NZ     0.32    2.38  INTRA BF
 116 HIS   ( 130-)  A      NE2 <->  139 GLU   ( 153-)  A      OE2    0.31    2.39  INTRA BL
 291 HIS   (  98-)  B      ND1 <-> 1240 SO4   ( 232-)  B      O1     0.30    2.40  INTRA BF
 778 SER   ( 175-)  D      OG  <->  780 HIS   ( 177-)  D      NE2    0.29    2.41  INTRA BL
   1 MET   (   1-)  A      C   <->    5 LYS   (   5-)  A      NZ     0.29    2.81  INTRA BF
 980 SER   ( 175-)  E      OG  <->  982 HIS   ( 177-)  E      NE2    0.27    2.43  INTRA BF
1056 ASP   (  44-)  F      CB  <-> 1248  ZN   ( 230-)  F     ZN      0.25    2.95  INTRA BF
 376 VAL   ( 183-)  B      CG1 <-> 1240 SO4   ( 232-)  B      O4     0.23    2.57  INTRA BF
 485 ASP   (  86-)  C      O   <->  488 LYS   (  89-)  C      NZ     0.23    2.47  INTRA BF
 786 VAL   ( 183-)  D      CG1 <-> 1245 SO4   ( 231-)  D      O4     0.22    2.58  INTRA BF
 184 ARG   ( 198-)  A      NH2 <-> 1234 SO4   ( 232-)  A      O1     0.22    2.48  INTRA BF
 148 SER   ( 162-)  A      OG  <->  311 ASN   ( 118-)  B      ND2    0.21    2.49  INTRA BL
 780 HIS   ( 177-)  D      ND1 <-> 1254 HOH   ( 242 )  D      O      0.21    2.49  INTRA BL
 491 HIS   (  92-)  C      NE2 <->  819 MET   (   1-)  E      CE     0.21    2.89  INTRA BF
 161 SER   ( 175-)  A      OG  <->  163 HIS   ( 177-)  A      NE2    0.20    2.50  INTRA BL
 819 MET   (   1-)  E      O   <->  821 LYS   (   3-)  E      N      0.20    2.50  INTRA BF
 529 HIS   ( 130-)  C      NE2 <->  552 GLU   ( 153-)  C      OE2    0.20    2.50  INTRA BL
 365 GLN   ( 172-)  B      NE2 <-> 1252 HOH   ( 253 )  B      O      0.20    2.50  INTRA BL
And so on for a total of 145 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

1058 ARG   (  46-)  F      -7.50
  32 ARG   (  46-)  A      -7.46
 239 ARG   (  46-)  B      -7.36
 649 ARG   (  46-)  D      -7.35
 838 GLN   (  33-)  E      -7.11
 851 ARG   (  46-)  E      -7.03
 445 ARG   (  46-)  C      -6.89
1045 GLN   (  33-)  F      -6.73
 431 ARG   (  17-)  C      -6.21
 635 ARG   (  17-)  D      -5.91
 224 ARG   (  17-)  B      -5.88
  17 ARG   (  17-)  A      -5.81
 835 ARG   (  17-)  E      -5.81
1042 ARG   (  17-)  F      -5.78
  86 ASN   ( 100-)  A      -5.41
 703 ASN   ( 100-)  D      -5.40
1230 GLU   ( 218-)  F      -5.26
 617 GLU   ( 218-)  C      -5.13
 739 LYS   ( 136-)  D      -5.11
 905 ASN   ( 100-)  E      -5.09
 293 ASN   ( 100-)  B      -5.05
1112 ASN   ( 100-)  F      -5.04

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: 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: 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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

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.

1251 HOH   ( 267 )  A      O      1.68   46.80   27.15

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.

1251 HOH   ( 266 )  A      O
Metal-coordinating Histidine residue  84 fixed to   1
Metal-coordinating Histidine residue 291 fixed to   1
Metal-coordinating Histidine residue 497 fixed to   1
Metal-coordinating Histidine residue 701 fixed to   1
Metal-coordinating Histidine residue 903 fixed to   1
Metal-coordinating Histidine residue1110 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.

 103 ASN   ( 117-)  A
 703 ASN   ( 100-)  D
1048 HIS   (  36-)  F
1066 ASN   (  54-)  F

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.

   4 ILE   (   4-)  A      N
  14 TRP   (  14-)  A      NE1
  32 ARG   (  46-)  A      N
  42 GLU   (  56-)  A      N
  55 GLN   (  69-)  A      NE2
  59 THR   (  73-)  A      N
  63 CYS   (  77-)  A      N
  78 HIS   (  92-)  A      N
  78 HIS   (  92-)  A      NE2
  97 LYS   ( 111-)  A      N
 110 ARG   ( 124-)  A      NE
 167 TYR   ( 181-)  A      OH
 211 ILE   (   4-)  B      N
 239 ARG   (  46-)  B      N
 249 GLU   (  56-)  B      N
 253 LEU   (  60-)  B      N
 270 CYS   (  77-)  B      N
 285 HIS   (  92-)  B      N
 304 LYS   ( 111-)  B      N
 306 LEU   ( 113-)  B      N
 317 ARG   ( 124-)  B      NE
 353 ARG   ( 160-)  B      NE
 353 ARG   ( 160-)  B      NH2
 412 ASN   ( 219-)  B      N
 413 ILE   ( 220-)  B      N
And so on for a total of 80 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.

 262 GLN   (  69-)  B      OE1
 695 HIS   (  92-)  D      NE2

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.

 383 ASP   ( 190-)  B   H-bonding suggests Asn; but Alt-Rotamer
 589 ASP   ( 190-)  C   H-bonding suggests Asn; but Alt-Rotamer
 995 ASP   ( 190-)  E   H-bonding suggests Asn; but Alt-Rotamer
1062 GLU   (  50-)  F   H-bonding suggests Gln; but Alt-Rotamer
1202 ASP   ( 190-)  F   H-bonding suggests Asn; 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 :   0.424
  2nd generation packing quality :  -1.031
  Ramachandran plot appearance   :  -0.337
  chi-1/chi-2 rotamer normality  :  -2.762
  Backbone conformation          :   0.480

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.482 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   1.047
  Side chain planarity           :   0.633 (tight)
  Improper dihedral distribution :   0.590
  B-factor distribution          :   0.357
  Inside/Outside distribution    :   1.024

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 :   1.2
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.482 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   1.047
  Side chain planarity           :   0.633 (tight)
  Improper dihedral distribution :   0.590
  B-factor distribution          :   0.357
  Inside/Outside distribution    :   1.024
==============

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.