WHAT IF Check report

This file was created 2011-12-18 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2ya4.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 : 0.540
CA-only RMS fit for the two chains : 0.298

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 943 FMT   (1777-)  A  -
 944 FMT   (1778-)  A  -
 945 EDO   (1779-)  A  -
 946 EDO   (1780-)  A  -
 947 EDO   (1781-)  A  -
 948 FMT   (1782-)  A  -
 949 FMT   (1783-)  A  -
 950 FMT   (1784-)  A  -
 952 FMT   (1785-)  A  -
 953 FMT   (1778-)  B  -
 954 FMT   (1779-)  B  -
 955 EDO   (1780-)  B  -
 956 EDO   (1781-)  B  -
 957 EDO   (1782-)  B  -
 958 FMT   (1783-)  B  -
 960 FMT   (1784-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 293 LYS   ( 599-)  A    0.10
 763 LYS   ( 599-)  B    0.10

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.466
RMS-deviation in bond distances: 0.011

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

 |  0.997014 -0.000264 -0.000478|
 | -0.000264  0.997299 -0.000722|
 | -0.000478 -0.000722  0.996840|
Proposed new scale matrix

 |  0.006064  0.000003  0.001576|
 |  0.000005  0.020520  0.000015|
 |  0.000004  0.000006  0.008274|
With corresponding cell

    A    = 164.932  B   =  48.732  C    = 124.889
    Alpha=  90.073  Beta= 104.595  Gamma=  90.030

The CRYST1 cell dimensions

    A    = 165.420  B   =  48.864  C    = 125.247
    Alpha=  90.000  Beta= 104.540  Gamma=  90.000

Variance: 281.655
(Under-)estimated Z-score: 12.369

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.

  48 HIS   ( 354-)  A      CG   ND1  CE1 109.65    4.0
 795 THR   ( 631-)  B      C    CA   CB  117.87    4.1

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.656
RMS-deviation in bond angles: 1.344

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.

 844 TYR   ( 680-)  B    -2.8
 374 TYR   ( 680-)  A    -2.8
  27 ILE   ( 333-)  A    -2.8
 497 ILE   ( 333-)  B    -2.6
 746 HIS   ( 582-)  B    -2.6
 276 HIS   ( 582-)  A    -2.6
 704 THR   ( 540-)  B    -2.5
 385 GLU   ( 691-)  A    -2.4
 529 ILE   ( 365-)  B    -2.3
  59 ILE   ( 365-)  A    -2.3
 894 ILE   ( 730-)  B    -2.2
 234 THR   ( 540-)  A    -2.2
 570 VAL   ( 406-)  B    -2.2
 845 VAL   ( 681-)  B    -2.2
 375 VAL   ( 681-)  A    -2.2
 382 THR   ( 688-)  A    -2.1
 100 VAL   ( 406-)  A    -2.1
 500 LEU   ( 336-)  B    -2.1
 795 THR   ( 631-)  B    -2.1
 518 HIS   ( 354-)  B    -2.1
 843 VAL   ( 679-)  B    -2.1
 215 LEU   ( 521-)  A    -2.0
 682 ASP   ( 518-)  B    -2.0
 325 THR   ( 631-)  A    -2.0
 212 ASP   ( 518-)  A    -2.0
 852 THR   ( 688-)  B    -2.0
 373 VAL   ( 679-)  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.

  14 ASN   ( 320-)  A  Poor phi/psi
  24 SER   ( 330-)  A  omega poor
  27 ILE   ( 333-)  A  Poor phi/psi
  42 ALA   ( 348-)  A  omega poor
  48 HIS   ( 354-)  A  Poor phi/psi
  59 ILE   ( 365-)  A  omega poor
  65 ASN   ( 371-)  A  Poor phi/psi
  89 ILE   ( 395-)  A  omega poor
  92 PRO   ( 398-)  A  omega poor
  93 VAL   ( 399-)  A  omega poor
  96 ASP   ( 402-)  A  Poor phi/psi
 106 LYS   ( 412-)  A  Poor phi/psi
 119 LYS   ( 425-)  A  Poor phi/psi
 157 ASN   ( 463-)  A  Poor phi/psi
 180 ALA   ( 486-)  A  Poor phi/psi
 181 TYR   ( 487-)  A  Poor phi/psi
 188 TYR   ( 494-)  A  omega poor
 206 PRO   ( 512-)  A  omega poor
 212 ASP   ( 518-)  A  Poor phi/psi
 223 ASP   ( 529-)  A  Poor phi/psi
 237 VAL   ( 543-)  A  Poor phi/psi
 243 LYS   ( 549-)  A  Poor phi/psi
 244 PHE   ( 550-)  A  omega poor
 247 VAL   ( 553-)  A  omega poor
 270 THR   ( 576-)  A  omega poor
And so on for a total of 93 lines.

Warning: Unusual backbone conformations

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

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

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

   9 PHE   ( 315-)  A      0
  13 ARG   ( 319-)  A      0
  19 LYS   ( 325-)  A      0
  26 ARG   ( 332-)  A      0
  27 ILE   ( 333-)  A      0
  28 PRO   ( 334-)  A      0
  35 LYS   ( 341-)  A      0
  46 ARG   ( 352-)  A      0
  47 LEU   ( 353-)  A      0
  48 HIS   ( 354-)  A      0
  51 ASP   ( 357-)  A      0
  52 TRP   ( 358-)  A      0
  54 ASP   ( 360-)  A      0
  57 MET   ( 363-)  A      0
  65 ASN   ( 371-)  A      0
  68 THR   ( 374-)  A      0
  72 ARG   ( 378-)  A      0
  76 THR   ( 382-)  A      0
  81 ASN   ( 387-)  A      0
  85 SER   ( 391-)  A      0
  89 ILE   ( 395-)  A      0
  91 SER   ( 397-)  A      0
  93 VAL   ( 399-)  A      0
  95 ILE   ( 401-)  A      0
  96 ASP   ( 402-)  A      0
And so on for a total of 444 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!

 403 GLY   ( 709-)  A   1.84   14
 718 GLY   ( 554-)  B   1.62   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]

 586 PRO   ( 422-)  B    0.18 LOW

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.

 383 MET   ( 689-)  A      CE  <->  388 GLU   ( 694-)  A      CA     0.31    2.89  INTRA BF
 852 THR   ( 688-)  B      OG1 <->  906 GLU   ( 742-)  B      OE2    0.27    2.13  INTRA BF
 149 LYS   ( 455-)  A      NZ  <->  961 HOH   (2153 )  A      O      0.26    2.44  INTRA
 619 LYS   ( 455-)  B      NZ  <->  962 HOH   (2145 )  B      O      0.22    2.48  INTRA
 929 SER   ( 765-)  B      OG  <->  962 HOH   (2415 )  B      O      0.18    2.22  INTRA
 898 GLU   ( 734-)  B      O   <->  918 HIS   ( 754-)  B      ND1    0.18    2.52  INTRA
 961 HOH   (2200 )  A      O   <->  962 HOH   (2321 )  B      O      0.17    2.23  INTRA BF
 836 ARG   ( 672-)  B      NH1 <->  962 HOH   (2367 )  B      O      0.16    2.54  INTRA BF
 851 HIS   ( 687-)  B      NE2 <->  858 GLU   ( 694-)  B      CG     0.15    2.95  INTRA
 876 HIS   ( 712-)  B      ND1 <->  891 HIS   ( 727-)  B      ND1    0.15    2.85  INTRA BF
 776 GLN   ( 612-)  B      NE2 <->  962 HOH   (2310 )  B      O      0.14    2.56  INTRA BF
 890 LYS   ( 726-)  B      NZ  <->  939 SER   ( 775-)  B      O      0.13    2.57  INTRA BF
 961 HOH   (2043 )  A      O   <->  961 HOH   (2045 )  A      O      0.13    2.07  INTRA
 961 HOH   (2153 )  A      O   <->  962 HOH   (2358 )  B      O      0.13    2.27  INTRA BF
 832 LYS   ( 668-)  B      O   <->  962 HOH   (2357 )  B      O      0.11    2.29  INTRA
 607 GLY   ( 443-)  B      N   <->  962 HOH   (2126 )  B      O      0.11    2.59  INTRA BF
 333 ASN   ( 639-)  A      N   <->  388 GLU   ( 694-)  A      OE2    0.11    2.59  INTRA
 873 GLY   ( 709-)  B      O   <->  894 ILE   ( 730-)  B      N      0.11    2.59  INTRA BF
 411 GLU   ( 717-)  A      C   <->  413 ASN   ( 719-)  A      N      0.10    2.80  INTRA BF
  23 LYS   ( 329-)  A      NZ  <->  961 HOH   (2023 )  A      O      0.09    2.61  INTRA
 625 ARG   ( 461-)  B      NH1 <->  962 HOH   (2155 )  B      O      0.09    2.61  INTRA
 384 HIS   ( 690-)  A      O   <->  389 TYR   ( 695-)  A      CE2    0.09    2.71  INTRA BF
 961 HOH   (2114 )  A      O   <->  962 HOH   (2315 )  B      O      0.09    2.31  INTRA BF
 203 LYS   ( 509-)  A      NZ  <->  951  CL   (1786-)  A     CL      0.08    3.02  INTRA BL
 806 ASP   ( 642-)  B      OD2 <->  962 HOH   (2341 )  B      O      0.08    2.32  INTRA
And so on for a total of 68 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 726 ARG   ( 562-)  B      -6.25
 256 ARG   ( 562-)  A      -6.24
  19 LYS   ( 325-)  A      -6.21
 489 LYS   ( 325-)  B      -6.21
 896 LYS   ( 732-)  B      -6.18
 412 GLU   ( 718-)  A      -5.72
 385 GLU   ( 691-)  A      -5.68
 426 LYS   ( 732-)  A      -5.62
 909 ASN   ( 745-)  B      -5.54
 814 LEU   ( 650-)  B      -5.36
 483 ARG   ( 319-)  B      -5.35
 362 LYS   ( 668-)  A      -5.16
  47 LEU   ( 353-)  A      -5.11
 344 LEU   ( 650-)  A      -5.06
 517 LEU   ( 353-)  B      -5.05
 882 GLU   ( 718-)  B      -5.01

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 164 ASP   ( 470-)  A   -2.63
 673 LYS   ( 509-)  B   -2.57
 203 LYS   ( 509-)  A   -2.53

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 961 HOH   (2242 )  A      O
Marked this atom as acceptor  951  CL  (1786-) A     CL
Marked this atom as acceptor  959  CL  (1785-) B     CL

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.

 547 ASN   ( 383-)  B
 776 GLN   ( 612-)  B

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  26 ARG   ( 332-)  A      NH2
  48 HIS   ( 354-)  A      N
  91 SER   ( 397-)  A      N
  94 ASN   ( 400-)  A      ND2
 213 SER   ( 519-)  A      N
 221 ASP   ( 527-)  A      N
 241 TRP   ( 547-)  A      N
 276 HIS   ( 582-)  A      NE2
 321 ARG   ( 627-)  A      NH2
 325 THR   ( 631-)  A      OG1
 342 ARG   ( 648-)  A      NE
 376 GLN   ( 682-)  A      N
 387 LYS   ( 693-)  A      N
 413 ASN   ( 719-)  A      N
 418 TRP   ( 724-)  A      N
 418 TRP   ( 724-)  A      NE1
 449 THR   ( 755-)  A      N
 453 GLN   ( 759-)  A      NE2
 466 GLU   ( 772-)  A      N
 496 ARG   ( 332-)  B      NH2
 518 HIS   ( 354-)  B      N
 522 TRP   ( 358-)  B      N
 561 SER   ( 397-)  B    A N
 564 ASN   ( 400-)  B      ND2
 588 GLY   ( 424-)  B      N
 623 THR   ( 459-)  B      OG1
 683 SER   ( 519-)  B      N
 691 ASP   ( 527-)  B      N
 711 TRP   ( 547-)  B      N
 730 HIS   ( 566-)  B      ND1
 741 THR   ( 577-)  B      OG1
 795 THR   ( 631-)  B      OG1
 812 ARG   ( 648-)  B      NE
 846 GLN   ( 682-)  B      N
 851 HIS   ( 687-)  B      NE2
 888 TRP   ( 724-)  B      NE1
 911 GLU   ( 747-)  B      N
 919 THR   ( 755-)  B      N
 936 GLU   ( 772-)  B      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.

  96 ASP   ( 402-)  A      OD1
 113 ASP   ( 419-)  A      OD2
 281 GLN   ( 587-)  A      OE1
 402 ASN   ( 708-)  A      OD1
 412 GLU   ( 718-)  A      OE1
 566 ASP   ( 402-)  B      OD1
 751 GLN   ( 587-)  B      OE1

Warning: Unusual water packing

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

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

 961 HOH   (2043 )  A      O  1.02 NA  6
 961 HOH   (2082 )  A      O  0.98  K  5 *2
 961 HOH   (2092 )  A      O  0.96  K  4 *2
 961 HOH   (2192 )  A      O  1.14  K  4 *2
 962 HOH   (2032 )  B      O  1.17  K  4 *2
 962 HOH   (2054 )  B      O  0.95 NA  6
 962 HOH   (2061 )  B      O  1.10  K  4 *2
 962 HOH   (2081 )  B      O  1.04  K  4 *2
 962 HOH   (2107 )  B      O  0.88  K  4 *2
 962 HOH   (2185 )  B      O  0.82  K  5 *2
 962 HOH   (2333 )  B      O  1.00  K  5 *2
 962 HOH   (2420 )  B      O  1.00  K  5 *2

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.

  51 ASP   ( 357-)  A   H-bonding suggests Asn; Ligand-contact
  54 ASP   ( 360-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
  64 ASP   ( 370-)  A   H-bonding suggests Asn; but Alt-Rotamer
  96 ASP   ( 402-)  A   H-bonding suggests Asn; Ligand-contact
 222 ASP   ( 528-)  A   H-bonding suggests Asn
 355 ASP   ( 661-)  A   H-bonding suggests Asn; but Alt-Rotamer
 372 ASP   ( 678-)  A   H-bonding suggests Asn; but Alt-Rotamer
 514 GLU   ( 350-)  B   H-bonding suggests Gln; Ligand-contact
 521 ASP   ( 357-)  B   H-bonding suggests Asn; Ligand-contact
 692 ASP   ( 528-)  B   H-bonding suggests Asn; Ligand-contact
 825 ASP   ( 661-)  B   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 :  -0.091
  2nd generation packing quality :  -0.919
  Ramachandran plot appearance   :  -0.495
  chi-1/chi-2 rotamer normality  :  -1.032
  Backbone conformation          :  -0.677

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.466 (tight)
  Bond angles                    :   0.656 (tight)
  Omega angle restraints         :   1.222
  Side chain planarity           :   0.472 (tight)
  Improper dihedral distribution :   0.659
  B-factor distribution          :   0.407
  Inside/Outside distribution    :   0.961

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.466 (tight)
  Bond angles                    :   0.656 (tight)
  Omega angle restraints         :   1.222
  Side chain planarity           :   0.472 (tight)
  Improper dihedral distribution :   0.659
  B-factor distribution          :   0.407
  Inside/Outside distribution    :   0.961
==============

WHAT IF
    G.Vriend,
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    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.