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 pdb1e8u.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 : 1.082
CA-only RMS fit for the two chains : 0.772

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: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
but NCS matrices (but not the unitary matrix) are found labeled `dont use`: 1
SEQRES multiplicity agrees with number of MTRIX matrices labeled `dont use`
Value of Z as found on the CRYST1 card: 4
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 8

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 99140.141
Volume of the Unit Cell V= 1138609.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
but the number of MTRIX matrices flagged as `do not use` = 1
which seems more or less consistent with the SEQRES multiplicity
because the unitary MTRIX record gets forgotten more often ...
Matthews coefficient for observed atoms and Z high: Vm= 5.742
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.850 Or should we use the previously suggested Z = 8
which would result in Vm= 2.871
And remember, a matrix counting problem has been reported earlier already

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.

 904 SLB   (1570-)  A  -
 909 SLB   (1573-)  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: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 897 GLU   ( 573-)  B
 447 GLY   ( 570-)  A

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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

 |  0.999272 -0.000189  0.000152|
 | -0.000189  0.998721 -0.000112|
 |  0.000152 -0.000112  0.998937|
Proposed new scale matrix

 |  0.013792  0.000003 -0.000002|
 |  0.000002  0.012756  0.000001|
 |  0.000000  0.000000  0.005007|
With corresponding cell

    A    =  72.506  B   =  78.393  C    = 199.708
    Alpha=  90.008  Beta=  89.992  Gamma=  90.022

The CRYST1 cell dimensions

    A    =  72.560  B   =  78.490  C    = 199.930
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 31.910
(Under-)estimated Z-score: 4.163

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.

 319 TYR   ( 442-)  A      N    CA   C    99.42   -4.2
 496 THR   ( 173-)  B      N    CA   C    99.00   -4.4

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.

 428 THR   ( 551-)  A    5.01
 319 TYR   ( 442-)  A    4.46
 496 THR   ( 173-)  B    4.41
 430 PHE   ( 553-)  A    4.25
 693 GLN   ( 370-)  B    4.23
 765 TYR   ( 442-)  B    4.14
 247 GLN   ( 370-)  A    4.04

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.

 344 THR   ( 467-)  A    -3.0
 790 THR   ( 467-)  B    -2.8
 777 PRO   ( 454-)  B    -2.6
 331 PRO   ( 454-)  A    -2.6
 822 LEU   ( 499-)  B    -2.5
 749 LEU   ( 426-)  B    -2.4
 350 PRO   ( 473-)  A    -2.4
 481 GLU   ( 158-)  B    -2.4
 188 ARG   ( 311-)  A    -2.3
 875 LEU   ( 552-)  B    -2.3
 874 THR   ( 551-)  B    -2.3
 770 PHE   ( 447-)  B    -2.2
 757 LYS   ( 434-)  B    -2.2
 511 THR   ( 188-)  B    -2.2
 114 SER   ( 237-)  A    -2.2
 324 PHE   ( 447-)  A    -2.2
 792 VAL   ( 469-)  B    -2.2
  65 THR   ( 188-)  A    -2.2
 346 VAL   ( 469-)  A    -2.2
 640 TYR   ( 317-)  B    -2.1
 519 CYS   ( 196-)  B    -2.1
  73 CYS   ( 196-)  A    -2.1
  66 HIS   ( 189-)  A    -2.0
 658 VAL   ( 335-)  B    -2.0
 194 TYR   ( 317-)  A    -2.0
 512 HIS   ( 189-)  B    -2.0
 152 LEU   ( 275-)  A    -2.0
 796 PRO   ( 473-)  B    -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.

   4 ILE   ( 127-)  A  Poor phi/psi
  31 SER   ( 154-)  A  Poor phi/psi
  75 ASP   ( 198-)  A  Poor phi/psi
 179 VAL   ( 302-)  A  Poor phi/psi
 200 ASN   ( 323-)  A  Poor phi/psi
 296 SER   ( 419-)  A  Poor phi/psi
 311 LYS   ( 434-)  A  Poor phi/psi
 330 ILE   ( 453-)  A  PRO omega poor
 344 THR   ( 467-)  A  Poor phi/psi
 359 HIS   ( 482-)  A  Poor phi/psi
 362 ARG   ( 485-)  A  Poor phi/psi
 370 ASP   ( 493-)  A  Poor phi/psi
 377 ASN   ( 500-)  A  Poor phi/psi
 386 THR   ( 509-)  A  Poor phi/psi
 395 SER   ( 518-)  A  Poor phi/psi
 415 ASN   ( 538-)  A  Poor phi/psi
 428 THR   ( 551-)  A  Poor phi/psi
 445 ASN   ( 568-)  A  Poor phi/psi
 449 PRO   ( 126-)  B  Poor phi/psi
 468 ALA   ( 145-)  B  Poor phi/psi
 477 SER   ( 154-)  B  Poor phi/psi
 480 GLN   ( 157-)  B  Poor phi/psi
 481 GLU   ( 158-)  B  Poor phi/psi
 554 ASP   ( 231-)  B  Poor phi/psi
 560 SER   ( 237-)  B  Poor phi/psi
 578 THR   ( 255-)  B  Poor phi/psi
 625 VAL   ( 302-)  B  Poor phi/psi
 646 ASN   ( 323-)  B  Poor phi/psi
 742 SER   ( 419-)  B  Poor phi/psi
 756 ASN   ( 433-)  B  Poor phi/psi
 776 ILE   ( 453-)  B  PRO omega poor
 790 THR   ( 467-)  B  Poor phi/psi
 805 HIS   ( 482-)  B  Poor phi/psi
 816 ASP   ( 493-)  B  Poor phi/psi
 823 ASN   ( 500-)  B  Poor phi/psi
 832 THR   ( 509-)  B  Poor phi/psi
 841 SER   ( 518-)  B  Poor phi/psi
 861 ASN   ( 538-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.754

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!

   3 PRO   ( 126-)  A      0
   4 ILE   ( 127-)  A      0
  10 ILE   ( 133-)  A      0
  13 ILE   ( 136-)  A      0
  17 LEU   ( 140-)  A      0
  20 ASP   ( 143-)  A      0
  21 ASN   ( 144-)  A      0
  23 SER   ( 146-)  A      0
  28 PHE   ( 151-)  A      0
  32 ALA   ( 155-)  A      0
  33 PHE   ( 156-)  A      0
  35 GLU   ( 158-)  A      0
  36 HIS   ( 159-)  A      0
  39 PHE   ( 162-)  A      0
  44 THR   ( 167-)  A      0
  51 ARG   ( 174-)  A      0
  52 ILE   ( 175-)  A      0
  53 PRO   ( 176-)  A      0
  66 HIS   ( 189-)  A      0
  70 LEU   ( 193-)  A      0
  71 SER   ( 194-)  A      0
  73 CYS   ( 196-)  A      0
  74 ARG   ( 197-)  A      0
  77 SER   ( 200-)  A      0
  78 HIS   ( 201-)  A      0
And so on for a total of 414 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.538

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.

 216 ARG   ( 339-)  A      NH2 <->  334 ALA   ( 457-)  A      O      0.34    2.36  INTRA BL
  85 LEU   ( 208-)  A      CD2 <->  124 CYS   ( 247-)  A      SG     0.34    3.06  INTRA BL
   5 HIS   ( 128-)  A      ND1 <->   88 LEU   ( 211-)  A      N      0.29    2.71  INTRA BF
 595 HIS   ( 272-)  B      ND1 <->  706 GLY   ( 383-)  B      N      0.25    2.75  INTRA BL
 657 TYR   ( 334-)  B      CE2 <->  679 LYS   ( 356-)  B      NZ     0.24    2.86  INTRA BF
 830 ASP   ( 507-)  B      OD1 <->  833 SER   ( 510-)  B      N      0.24    2.46  INTRA
 675 ILE   ( 352-)  B      CG2 <->  679 LYS   ( 356-)  B      NZ     0.22    2.88  INTRA BF
 375 ARG   ( 498-)  A      NH2 <->  902 SLB   (1570-)  A      O1A    0.22    2.48  INTRA
 217 TYR   ( 340-)  A      CZ  <->  218 ASN   ( 341-)  A      ND2    0.21    2.89  INTRA
 224 GLU   ( 347-)  A      CD  <->  225 GLN   ( 348-)  A      N      0.21    2.79  INTRA
 873 ASN   ( 550-)  B      CG  <->  876 PHE   ( 553-)  B      CD1    0.21    2.99  INTRA BF
  74 ARG   ( 197-)  A      O   <->   76 HIS   ( 199-)  A      N      0.20    2.50  INTRA BF
  42 ALA   ( 165-)  A      CB  <->  434 ARG   ( 557-)  A      NH2    0.20    2.90  INTRA
 451 HIS   ( 128-)  B      CD2 <->  534 LEU   ( 211-)  B      N      0.20    2.90  INTRA BL
 477 SER   ( 154-)  B      N   <->  886 VAL   ( 563-)  B      CG2    0.18    2.92  INTRA
 506 THR   ( 183-)  B      OG1 <->  507 HIS   ( 184-)  B      ND1    0.18    2.52  INTRA BL
 411 VAL   ( 534-)  A      O   <->  415 ASN   ( 538-)  A      N      0.17    2.53  INTRA
 742 SER   ( 419-)  B      C   <->  788 CYS   ( 465-)  B      SG     0.16    3.24  INTRA
 466 ASP   ( 143-)  B      O   <->  808 ARG   ( 485-)  B      NH1    0.15    2.55  INTRA BF
 384 ASP   ( 507-)  A      OD1 <->  387 SER   ( 510-)  A      N      0.15    2.55  INTRA BL
 717 THR   ( 394-)  B      N   <->  718 VAL   ( 395-)  B      N      0.15    2.45  INTRA B3
 388 ARG   ( 511-)  A      NH1 <->  391 ILE   ( 514-)  A      CG2    0.15    2.95  INTRA
 271 THR   ( 394-)  A      N   <->  272 VAL   ( 395-)  A      N      0.15    2.45  INTRA BL
  74 ARG   ( 197-)  A      C   <->   76 HIS   ( 199-)  A      N      0.14    2.76  INTRA BF
 141 SER   ( 264-)  A      CB  <->  901  CA   (1002-)  A     CA      0.14    3.06  INTRA
And so on for a total of 105 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.

 217 TYR   ( 340-)  A      -7.07
 663 TYR   ( 340-)  B      -7.00
 337 ARG   ( 460-)  A      -6.09
 522 HIS   ( 199-)  B      -5.95
 390 ARG   ( 513-)  A      -5.79
 240 ARG   ( 363-)  A      -5.66
 524 HIS   ( 201-)  B      -5.63
 783 ARG   ( 460-)  B      -5.56
 686 ARG   ( 363-)  B      -5.51
  78 HIS   ( 201-)  A      -5.49
 836 ARG   ( 513-)  B      -5.26
 218 ASN   ( 341-)  A      -5.23
  76 HIS   ( 199-)  A      -5.23
 154 PHE   ( 277-)  A      -5.10
 600 PHE   ( 277-)  B      -5.07
 772 ARG   ( 449-)  B      -5.06
 330 ILE   ( 453-)  A      -5.06
 586 ASN   ( 263-)  B      -5.00

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.

 170 GLU   ( 293-)  A   -2.87
 446 ASP   ( 569-)  A   -2.70
 374 ALA   ( 497-)  A   -2.60
 552 LEU   ( 229-)  B   -2.51

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

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.

 908 HOH   (2041 )  A      O     33.77   38.51   61.28

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.

 908 HOH   (2073 )  A      O
 908 HOH   (2099 )  A      O
 908 HOH   (2165 )  A      O
 908 HOH   (2231 )  A      O
Bound group on Asn; dont flip  358 ASN  ( 481-) A
Bound to:  897 NAG  (1572-) A
Bound group on Asn; dont flip  804 ASN  ( 481-) B
Bound to:  899 NAG  (1574-) B

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.

  80 HIS   ( 203-)  A
 110 GLN   ( 233-)  A
 200 ASN   ( 323-)  A
 248 GLN   ( 371-)  A
 292 GLN   ( 415-)  A
 359 HIS   ( 482-)  A
 373 GLN   ( 496-)  A
 445 ASN   ( 568-)  A
 451 HIS   ( 128-)  B
 467 ASN   ( 144-)  B
 674 GLN   ( 351-)  B
 823 ASN   ( 500-)  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.

   4 ILE   ( 127-)  A      N
   5 HIS   ( 128-)  A      N
  37 LEU   ( 160-)  A      N
  61 HIS   ( 184-)  A      N
  64 TYR   ( 187-)  A      OH
  74 ARG   ( 197-)  A      NE
  76 HIS   ( 199-)  A      N
  79 SER   ( 202-)  A      N
  95 ARG   ( 218-)  A      NE
  96 ILE   ( 219-)  A      N
 110 GLN   ( 233-)  A      N
 132 THR   ( 255-)  A      N
 133 GLU   ( 256-)  A      N
 136 GLU   ( 259-)  A      N
 147 MET   ( 270-)  A      N
 211 TYR   ( 334-)  A      N
 221 CYS   ( 344-)  A      N
 261 GLU   ( 384-)  A      N
 333 GLN   ( 456-)  A      N
 340 ASN   ( 463-)  A      N
 346 VAL   ( 469-)  A      N
 403 TYR   ( 526-)  A      N
 408 CYS   ( 531-)  A      N
 454 ASP   ( 131-)  B      N
 483 LEU   ( 160-)  B      N
 485 PHE   ( 162-)  B      N
 522 HIS   ( 199-)  B      N
 579 GLU   ( 256-)  B      N
 582 GLU   ( 259-)  B      N
 593 MET   ( 270-)  B      N
 661 LYS   ( 338-)  B      N
 672 ASP   ( 349-)  B      N
 739 ARG   ( 416-)  B      NH1
 779 GLN   ( 456-)  B      N
 786 ASN   ( 463-)  B      N
 792 VAL   ( 469-)  B      N
 808 ARG   ( 485-)  B      NH1
 844 SER   ( 521-)  B      N
 845 THR   ( 522-)  B      OG1
 854 CYS   ( 531-)  B      N
 874 THR   ( 551-)  B      N
 880 ARG   ( 557-)  B      NH1
 894 VAL   ( 571-)  B      N
 895 ARG   ( 572-)  B      NE
Only metal coordination for  584 ASP  ( 261-) B      OD1

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.

  35 GLU   ( 158-)  A      OE2
 581 GLU   ( 258-)  B      OE2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  20 ASP   ( 143-)  A   H-bonding suggests Asn; but Alt-Rotamer
  56 ASP   ( 179-)  A   H-bonding suggests Asn
 502 ASP   ( 179-)  B   H-bonding suggests Asn; but Alt-Rotamer
 581 GLU   ( 258-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact

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 :  -0.475
  2nd generation packing quality :  -1.560
  Ramachandran plot appearance   :  -1.534
  chi-1/chi-2 rotamer normality  :  -1.754
  Backbone conformation          :  -0.516

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.282 (tight)
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   0.280 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.615
  B-factor distribution          :   0.411
  Inside/Outside distribution    :   1.016

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.282 (tight)
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   0.280 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.615
  B-factor distribution          :   0.411
  Inside/Outside distribution    :   1.016
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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      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,
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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.