WHAT IF Check report

This file was created 2012-01-30 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 pdb3mdy.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: B and D

All-atom RMS fit for the two chains : 0.203
CA-only RMS fit for the two chains : 0.037

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.

 859 LDN   (   1-)  A  -
 860 LDN   (   1-)  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: C

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: D

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'.

   1 GLU   ( 174-)  A      CG
   1 GLU   ( 174-)  A      CD
   1 GLU   ( 174-)  A      OE1
   1 GLU   ( 174-)  A      OE2
   4 ARG   ( 177-)  A      CG
   4 ARG   ( 177-)  A      CD
   4 ARG   ( 177-)  A      NE
   4 ARG   ( 177-)  A      CZ
   4 ARG   ( 177-)  A      NH1
   4 ARG   ( 177-)  A      NH2
 150 GLN   ( 323-)  A      CG
 150 GLN   ( 323-)  A      CD
 150 GLN   ( 323-)  A      OE1
 150 GLN   ( 323-)  A      NE2
 169 LYS   ( 342-)  A      CE
 169 LYS   ( 342-)  A      NZ
 185 ILE   ( 358-)  A      CG1
 185 ILE   ( 358-)  A      CG2
 185 ILE   ( 358-)  A      CD1
 314 GLU   ( 496-)  A      CD
 314 GLU   ( 496-)  A      OE1
 314 GLU   ( 496-)  A      OE2
 319 LYS   ( 501-)  A      CG
 319 LYS   ( 501-)  A      CD
 319 LYS   ( 501-)  A      CE
And so on for a total of 75 lines.

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.

   2 SER   ( 175-)  A    High
   8 GLU   ( 181-)  A    High
  51 ARG   ( 224-)  A    High
 322 SER   ( 175-)  C    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: 12

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.529 over 6009 bonds
Average difference in B over a bond : 4.20
RMS difference in B over a bond : 5.81

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: C

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: D

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.

  41 ARG   ( 214-)  A
 189 ARG   ( 371-)  A
 207 ARG   ( 389-)  A
 230 ARG   ( 412-)  A
 282 ARG   ( 464-)  A
 304 ARG   ( 486-)  A
 361 ARG   ( 214-)  C
 371 ARG   ( 224-)  C
 401 ARG   ( 254-)  C
 511 ARG   ( 371-)  C
 529 ARG   ( 389-)  C
 552 ARG   ( 412-)  C
 604 ARG   ( 464-)  C
 660 ARG   (  19-)  B
 682 ARG   (  41-)  B
 699 ARG   (  58-)  B
 769 ARG   (  19-)  D
 791 ARG   (  41-)  D
 808 ARG   (  58-)  D

Warning: Tyrosine convention problem

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

 195 TYR   ( 377-)  A
 219 TYR   ( 401-)  A
 517 TYR   ( 377-)  C
 541 TYR   ( 401-)  C
 668 TYR   (  27-)  B
 777 TYR   (  27-)  D

Warning: Phenylalanine convention problem

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

  60 PHE   ( 233-)  A
 184 PHE   ( 357-)  A
 271 PHE   ( 453-)  A
 380 PHE   ( 233-)  C
 593 PHE   ( 453-)  C
 657 PHE   (  16-)  B
 690 PHE   (  49-)  B
 766 PHE   (  16-)  D
 799 PHE   (  49-)  D

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.

 317 ASP   ( 499-)  A

Warning: Glutamic acid convention problem

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

  53 GLU   ( 226-)  A
  64 GLU   ( 237-)  A
  65 GLU   ( 238-)  A
  73 GLU   ( 246-)  A
 145 GLU   ( 318-)  A
 239 GLU   ( 421-)  A
 279 GLU   ( 461-)  A
 373 GLU   ( 226-)  C
 384 GLU   ( 237-)  C
 385 GLU   ( 238-)  C
 393 GLU   ( 246-)  C
 465 GLU   ( 318-)  C
 561 GLU   ( 421-)  C
 601 GLU   ( 461-)  C
 647 GLU   (   6-)  B
 673 GLU   (  32-)  B
 702 GLU   (  61-)  B
 703 GLU   (  62-)  B
 756 GLU   (   6-)  D
 782 GLU   (  32-)  D
 811 GLU   (  61-)  D
 812 GLU   (  62-)  D

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 707 GLN   (  66-)  B      CD   NE2   1.24   -4.0

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

 |  0.997767 -0.000026  0.000186|
 | -0.000026  0.998429 -0.000134|
 |  0.000186 -0.000134  0.998870|
Proposed new scale matrix

 |  0.015322  0.000000 -0.000003|
 |  0.000000  0.012518  0.000002|
 | -0.000001  0.000000  0.005461|
With corresponding cell

    A    =  65.265  B   =  79.887  C    = 183.111
    Alpha=  90.009  Beta=  89.979  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  65.410  B   =  80.010  C    = 183.330
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 79.061
(Under-)estimated Z-score: 6.553

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.

  80 MET   ( 253-)  A      CG   SD   CE   91.54   -4.3
 429 HIS   ( 282-)  C      CG   ND1  CE1 109.62    4.0
 463 HIS   ( 316-)  C      CG   ND1  CE1 109.68    4.1

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.

  41 ARG   ( 214-)  A
  53 GLU   ( 226-)  A
  64 GLU   ( 237-)  A
  65 GLU   ( 238-)  A
  73 GLU   ( 246-)  A
 145 GLU   ( 318-)  A
 189 ARG   ( 371-)  A
 207 ARG   ( 389-)  A
 230 ARG   ( 412-)  A
 239 GLU   ( 421-)  A
 279 GLU   ( 461-)  A
 282 ARG   ( 464-)  A
 304 ARG   ( 486-)  A
 317 ASP   ( 499-)  A
 361 ARG   ( 214-)  C
 371 ARG   ( 224-)  C
 373 GLU   ( 226-)  C
 384 GLU   ( 237-)  C
 385 GLU   ( 238-)  C
 393 GLU   ( 246-)  C
 401 ARG   ( 254-)  C
 465 GLU   ( 318-)  C
 511 ARG   ( 371-)  C
 529 ARG   ( 389-)  C
 552 ARG   ( 412-)  C
 561 GLU   ( 421-)  C
 601 GLU   ( 461-)  C
 604 ARG   ( 464-)  C
 647 GLU   (   6-)  B
 660 ARG   (  19-)  B
 673 GLU   (  32-)  B
 682 ARG   (  41-)  B
 699 ARG   (  58-)  B
 702 GLU   (  61-)  B
 703 GLU   (  62-)  B
 756 GLU   (   6-)  D
 769 ARG   (  19-)  D
 782 GLU   (  32-)  D
 791 ARG   (  41-)  D
 808 ARG   (  58-)  D
 811 GLU   (  61-)  D
 812 GLU   (  62-)  D

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.

 149 THR   ( 322-)  A    -2.4
 656 THR   (  15-)  B    -2.4
  42 TYR   ( 215-)  A    -2.3
 362 TYR   ( 215-)  C    -2.3
 765 THR   (  15-)  D    -2.3
  15 SER   ( 188-)  A    -2.3
 469 THR   ( 322-)  C    -2.2
 238 VAL   ( 420-)  A    -2.2
 560 VAL   ( 420-)  C    -2.1
 335 SER   ( 188-)  C    -2.1
  77 THR   ( 250-)  A    -2.1
 497 ASP   ( 350-)  C    -2.1
 177 ASP   ( 350-)  A    -2.0
 121 THR   ( 294-)  A    -2.0
 424 LEU   ( 277-)  C    -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.

  15 SER   ( 188-)  A  Poor phi/psi
  26 THR   ( 199-)  A  omega poor
  42 TYR   ( 215-)  A  Poor phi/psi
  46 TRP   ( 219-)  A  omega poor
  60 PHE   ( 233-)  A  omega poor
  79 LEU   ( 252-)  A  Poor phi/psi
  81 ARG   ( 254-)  A  omega poor
  95 GLY   ( 268-)  A  omega poor
 123 LEU   ( 296-)  A  omega poor
 158 ARG   ( 331-)  A  Poor phi/psi
 177 ASP   ( 350-)  A  Poor phi/psi
 203 GLU   ( 385-)  A  Poor phi/psi
 245 TYR   ( 427-)  A  Poor phi/psi
 317 ASP   ( 499-)  A  Poor phi/psi
 322 SER   ( 175-)  C  omega poor
 333 SER   ( 186-)  C  Poor phi/psi
 335 SER   ( 188-)  C  Poor phi/psi
 346 THR   ( 199-)  C  omega poor
 351 ILE   ( 204-)  C  omega poor
 362 TYR   ( 215-)  C  Poor phi/psi
 366 TRP   ( 219-)  C  omega poor
 399 LEU   ( 252-)  C  Poor phi/psi
 401 ARG   ( 254-)  C  omega poor
 424 LEU   ( 277-)  C  omega poor
 443 LEU   ( 296-)  C  omega poor
 478 ARG   ( 331-)  C  Poor phi/psi
 497 ASP   ( 350-)  C  Poor phi/psi
 525 GLU   ( 385-)  C  Poor phi/psi
 567 TYR   ( 427-)  C  Poor phi/psi
 639 ASP   ( 499-)  C  Poor phi/psi
 655 ARG   (  14-)  B  Poor phi/psi
 666 VAL   (  25-)  B  omega poor
 668 TYR   (  27-)  B  omega poor
 695 GLN   (  54-)  B  Poor phi/psi
 723 ALA   (  82-)  B  Poor phi/psi
 736 HIS   (  95-)  B  Poor phi/psi
 737 ALA   (  96-)  B  omega poor
 746 LEU   ( 105-)  B  omega poor
 764 ARG   (  14-)  D  Poor phi/psi
 775 VAL   (  25-)  D  omega poor
 777 TYR   (  27-)  D  omega poor
 804 GLN   (  54-)  D  Poor phi/psi
 832 ALA   (  82-)  D  Poor phi/psi
 833 TYR   (  83-)  D  omega poor
 845 HIS   (  95-)  D  Poor phi/psi
 846 ALA   (  96-)  D  omega poor
 855 LEU   ( 105-)  D  omega poor
 chi-1/chi-2 correlation Z-score : -1.414

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.

 313 SER   ( 495-)  A    0.34
 455 SER   ( 308-)  C    0.35
 135 SER   ( 308-)  A    0.36
 635 SER   ( 495-)  C    0.37
 127 SER   ( 300-)  A    0.40
 447 SER   ( 300-)  C    0.40

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  13 SER   ( 186-)  A      0
  15 SER   ( 188-)  A      0
  17 SER   ( 190-)  A      0
  19 LEU   ( 192-)  A      0
  33 MET   ( 206-)  A      0
  34 VAL   ( 207-)  A      0
  39 LYS   ( 212-)  A      0
  41 ARG   ( 214-)  A      0
  42 TYR   ( 215-)  A      0
  50 TRP   ( 223-)  A      0
  51 ARG   ( 224-)  A      0
  54 LYS   ( 227-)  A      0
  78 VAL   ( 251-)  A      0
  79 LEU   ( 252-)  A      0
  81 ARG   ( 254-)  A      0
  82 HIS   ( 255-)  A      0
  89 ILE   ( 262-)  A      0
  92 ASP   ( 265-)  A      0
  94 LYS   ( 267-)  A      0
  96 THR   ( 269-)  A      0
  99 TRP   ( 272-)  A      0
 107 ASP   ( 280-)  A      0
 111 ASN   ( 284-)  A      0
 113 SER   ( 286-)  A      0
 120 SER   ( 293-)  A      0
And so on for a total of 321 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!

 417 GLY   ( 270-)  C   1.64   13

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]

  20 PRO   ( 193-)  A    0.19 LOW
 507 PRO   ( 367-)  C    0.17 LOW
 720 PRO   (  79-)  B    0.19 LOW
 829 PRO   (  79-)  D    0.18 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].

 198 PRO   ( 380-)  A  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 520 PRO   ( 380-)  C  -121.1 half-chair C-delta/C-gamma (-126 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.

 845 HIS   (  95-)  D      ND1 <->  864 HOH   ( 474 )  D      O      0.33    2.37  INTRA BF
 143 HIS   ( 316-)  A      CD2 <->  214 ILE   ( 396-)  A      CD1    0.28    2.92  INTRA
 463 HIS   ( 316-)  C      CD2 <->  536 ILE   ( 396-)  C      CD1    0.26    2.94  INTRA
 145 GLU   ( 318-)  A      OE2 <->  861 HOH   ( 670 )  A      O      0.24    2.16  INTRA BF
 158 ARG   ( 331-)  A      NH2 <->  187 ASN   ( 369-)  A      O      0.24    2.46  INTRA BF
  76 GLN   ( 249-)  A      NE2 <->  730 PRO   (  89-)  B      O      0.23    2.47  INTRA
 800 MET   (  50-)  D      SD  <->  803 LYS   (  53-)  D      NZ     0.23    3.07  INTRA BF
 403 GLU   ( 256-)  C      O   <->  488 LYS   ( 341-)  C      NZ     0.22    2.48  INTRA BL
 401 ARG   ( 254-)  C      NH2 <->  862 HOH   ( 129 )  C      O      0.21    2.49  INTRA
  83 GLU   ( 256-)  A      O   <->  168 LYS   ( 341-)  A      NZ     0.21    2.49  INTRA BL
 256 GLU   ( 438-)  A      CD  <->  861 HOH   ( 728 )  A      O      0.20    2.60  INTRA BF
  81 ARG   ( 254-)  A      NH2 <->  861 HOH   ( 523 )  A      O      0.19    2.51  INTRA
 294 HIS   ( 476-)  A      ND1 <->  861 HOH   ( 530 )  A      O      0.17    2.53  INTRA BL
 211 GLN   ( 393-)  A      OE1 <->  861 HOH   ( 505 )  A      O      0.16    2.24  INTRA BF
 616 HIS   ( 476-)  C      ND1 <->  862 HOH   ( 609 )  C      O      0.15    2.55  INTRA
 861 HOH   ( 617 )  A      O   <->  861 HOH   ( 670 )  A      O      0.15    2.05  INTRA
 653 ASP   (  12-)  B      OD1 <->  655 ARG   (  14-)  B      N      0.15    2.55  INTRA BF
 211 GLN   ( 393-)  A      CG  <->  861 HOH   ( 521 )  A      O      0.14    2.66  INTRA BF
 798 LYS   (  48-)  D      NZ  <->  858 GLU   ( 108-)  D      OE2    0.13    2.57  INTRA BF
 581 ARG   ( 441-)  C      NE  <->  862 HOH   ( 596 )  C      O      0.12    2.58  INTRA BF
 478 ARG   ( 331-)  C      NH2 <->  509 ASN   ( 369-)  C      O      0.11    2.59  INTRA
 331 GLN   ( 184-)  C      OE1 <->  338 GLY   ( 191-)  C      N      0.11    2.59  INTRA BF
  77 THR   ( 250-)  A      CG2 <->   78 VAL   ( 251-)  A      N      0.11    2.89  INTRA BF
  58 LYS   ( 231-)  A      NZ  <->   71 GLU   ( 244-)  A      OE1    0.11    2.59  INTRA BL
 158 ARG   ( 331-)  A      NH2 <->  861 HOH   ( 560 )  A      O      0.10    2.60  INTRA
And so on for a total of 90 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

  81 ARG   ( 254-)  A      -6.69
 147 PHE   ( 320-)  A      -6.68
 467 PHE   ( 320-)  C      -6.64
 401 ARG   ( 254-)  C      -6.54
 371 ARG   ( 224-)  C      -6.44
  51 ARG   ( 224-)  A      -6.44
 189 ARG   ( 371-)  A      -6.32
 511 ARG   ( 371-)  C      -6.23
 660 ARG   (  19-)  B      -6.14
 769 ARG   (  19-)  D      -6.06
 616 HIS   ( 476-)  C      -5.84
 294 HIS   ( 476-)  A      -5.84
 361 ARG   ( 214-)  C      -5.83
 184 PHE   ( 357-)  A      -5.79
  41 ARG   ( 214-)  A      -5.77
  39 LYS   ( 212-)  A      -5.74
 359 LYS   ( 212-)  C      -5.66
 691 MET   (  50-)  B      -5.66
 489 LYS   ( 342-)  C      -5.58
 110 GLU   ( 283-)  A      -5.56
 504 PHE   ( 357-)  C      -5.46
  42 TYR   ( 215-)  A      -5.44
 350 GLN   ( 203-)  C      -5.39
  30 GLN   ( 203-)  A      -5.38
 362 TYR   ( 215-)  C      -5.38
 782 GLU   (  32-)  D      -5.26
 673 GLU   (  32-)  B      -5.25
  99 TRP   ( 272-)  A      -5.15
 430 GLU   ( 283-)  C      -5.13
 419 TRP   ( 272-)  C      -5.08
 833 TYR   (  83-)  D      -5.05

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.

  12 SER   ( 185-)  A        14 - GLY    187- ( A)         -4.23
 147 PHE   ( 320-)  A       149 - THR    322- ( A)         -5.24
 467 PHE   ( 320-)  C       469 - THR    322- ( C)         -5.23

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: 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: 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: D

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.

 655 ARG   (  14-)  B   -2.92
 150 GLN   ( 323-)  A   -2.86
 470 GLN   ( 323-)  C   -2.85
 319 LYS   ( 501-)  A   -2.70

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: C

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: D

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.

 861 HOH   ( 693 )  A      O     24.82  -13.71   36.91

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.

 861 HOH   ( 589 )  A      O
 861 HOH   ( 644 )  A      O
 861 HOH   ( 671 )  A      O
 861 HOH   ( 679 )  A      O
 861 HOH   ( 691 )  A      O
 861 HOH   ( 694 )  A      O
 861 HOH   ( 722 )  A      O
 862 HOH   ( 576 )  C      O
 863 HOH   ( 566 )  B      O
 863 HOH   ( 656 )  B      O
 864 HOH   ( 345 )  D      O
 864 HOH   ( 642 )  D      O
 864 HOH   ( 655 )  D      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.

 101 GLN   ( 274-)  A
 421 GLN   ( 274-)  C
 431 ASN   ( 284-)  C

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.

  51 ARG   ( 224-)  A      NE
  82 HIS   ( 255-)  A      ND1
  84 ASN   ( 257-)  A      N
 109 HIS   ( 282-)  A      N
 161 LYS   ( 334-)  A      N
 188 THR   ( 370-)  A      OG1
 266 LYS   ( 448-)  A      N
 275 TRP   ( 457-)  A      NE1
 293 ALA   ( 475-)  A      N
 356 GLN   ( 209-)  C      N
 395 TYR   ( 248-)  C      OH
 401 ARG   ( 254-)  C      NH1
 429 HIS   ( 282-)  C      N
 470 GLN   ( 323-)  C      N
 474 ALA   ( 327-)  C      N
 481 LYS   ( 334-)  C      N
 588 LYS   ( 448-)  C      N
 597 TRP   ( 457-)  C      NE1
 615 ALA   ( 475-)  C      N
 639 ASP   ( 499-)  C      N
 654 GLY   (  13-)  B      N
 663 THR   (  22-)  B      N
 684 ARG   (  43-)  B      N
 701 TRP   (  60-)  B      NE1
 721 ASP   (  80-)  B      N
 724 TYR   (  83-)  B      OH
 763 GLY   (  13-)  D      N
 806 VAL   (  56-)  D      N
 808 ARG   (  58-)  D      NH2
 810 TRP   (  60-)  D      NE1
 830 ASP   (  80-)  D      N
 833 TYR   (  83-)  D      OH

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 861 HOH   ( 549 )  A      O  1.03  K  4
 861 HOH   ( 604 )  A      O  1.04  K  4

Warning: Possible wrong residue type

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

   8 GLU   ( 181-)  A   H-bonding suggests Gln
 202 ASP   ( 384-)  A   H-bonding suggests Asn; but Alt-Rotamer
 524 ASP   ( 384-)  C   H-bonding suggests Asn

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 :  -0.557
  2nd generation packing quality :  -0.971
  Ramachandran plot appearance   :  -0.254
  chi-1/chi-2 rotamer normality  :  -1.414
  Backbone conformation          :  -0.027

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.644 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   1.091
  Side chain planarity           :   0.629 (tight)
  Improper dihedral distribution :   0.762
  B-factor distribution          :   1.529 (loose)
  Inside/Outside distribution    :   1.004

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.644 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   1.091
  Side chain planarity           :   0.629 (tight)
  Improper dihedral distribution :   0.762
  B-factor distribution          :   1.529 (loose)
  Inside/Outside distribution    :   1.004
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
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      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    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.