WHAT IF Check report

This file was created 2014-12-18 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 pdb3tgs.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 : 0.339
CA-only RMS fit for the two chains : 0.266

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.

 706 03G   ( 507-)  A  -
 707 03G   ( 502-)  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: B-factors outside the range 0.0 - 100.0

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

   1 VAL   (  44-)  A    High
   2 TRP   (  45-)  A    High
   3 LYS   (  46-)  A    High
   4 GLU   (  47-)  A    High
   5 ALA   (  48-)  A    High
   6 LYS   (  49-)  A    High
   7 THR   (  50-)  A    High
  11 CYS   (  54-)  A    High
  14 ASP   (  57-)  A    High
  21 GLU   (  64-)  A    High
  34 THR   (  77-)  A    High
  35 ASP   (  78-)  A    High
  36 PRO   (  79-)  A    High
  37 ASN   (  80-)  A    High
  38 PRO   (  81-)  A    High
  39 GLN   (  82-)  A    High
  40 GLU   (  83-)  A    High
  41 MET   (  84-)  A    High
  42 VAL   (  85-)  A    High
  43 LEU   (  86-)  A    High
  44 ALA   (  87-)  A    High
  45 ASN   (  88-)  A    High
  46 VAL   (  89-)  A    High
  47 THR   (  90-)  A    High
  48 GLU   (  91-)  A    High
And so on for a total of 211 lines.

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: 8

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 : 1.511 over 3811 bonds
Average difference in B over a bond : 5.10
RMS difference in B over a bond : 6.95

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

Nomenclature related problems

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.

  40 GLU   (  83-)  A
  48 GLU   (  91-)  A
 152 GLU   ( 268-)  A
 174 GLU   ( 290-)  A
 385 GLU   (  83-)  B
 393 GLU   (  91-)  B
 497 GLU   ( 268-)  B

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.

 171 HIS   ( 287-)  A      CG   ND1   1.26   -6.3

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.

 171 HIS   ( 287-)  A      CG   ND1  CE1 110.35    4.8

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  40 GLU   (  83-)  A
  48 GLU   (  91-)  A
 152 GLU   ( 268-)  A
 174 GLU   ( 290-)  A
 385 GLU   (  83-)  B
 393 GLU   (  91-)  B
 497 GLU   ( 268-)  B

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.314

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.

 663 THR   ( 465-)  B    -3.3
 318 THR   ( 465-)  A    -3.2
 381 PRO   (  79-)  B    -2.9
  36 PRO   (  79-)  A    -2.9
 607 THR   ( 406-)  B    -2.8
 262 THR   ( 406-)  A    -2.7
 559 PRO   ( 354-)  B    -2.7
 120 THR   ( 236-)  A    -2.6
 116 THR   ( 232-)  A    -2.6
  38 PRO   (  81-)  A    -2.6
 461 THR   ( 232-)  B    -2.5
  80 THR   ( 123-)  A    -2.4
 181 THR   ( 297-)  A    -2.4
 280 ILE   ( 424-)  A    -2.4
 603 THR   ( 399-)  B    -2.3
 526 THR   ( 297-)  B    -2.3
 482 PRO   ( 253-)  B    -2.3
 532 ARG   ( 327-)  B    -2.2
 591 THR   ( 387-)  B    -2.2
  92 VAL   ( 208-)  A    -2.1
 326 GLY   ( 473-)  A    -2.1
 254 TYR   ( 395-)  A    -2.1
 474 VAL   ( 245-)  B    -2.1
 465 THR   ( 236-)  B    -2.1
 258 THR   ( 399-)  A    -2.1
 224 SER   ( 365-)  A    -2.1
 174 GLU   ( 290-)  A    -2.0
 383 PRO   (  81-)  B    -2.0
 580 PHE   ( 376-)  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.

  35 ASP   (  78-)  A  PRO omega poor
  45 ASN   (  88-)  A  Poor phi/psi
  72 SER   ( 115-)  A  Poor phi/psi
  87 GLN   ( 203-)  A  Poor phi/psi
 142 GLN   ( 258-)  A  Poor phi/psi
 152 GLU   ( 268-)  A  Poor phi/psi
 215 SER   ( 356-)  A  Poor phi/psi
 238 ARG   ( 379-)  A  Poor phi/psi
 239 GLY   ( 380-)  A  Poor phi/psi
 256 ASN   ( 397-)  A  Poor phi/psi
 261 HIS   ( 405-)  A  Poor phi/psi
 262 THR   ( 406-)  A  Poor phi/psi
 317 ASP   ( 464-)  A  Poor phi/psi
 380 ASP   (  78-)  B  PRO omega poor
 383 PRO   (  81-)  B  Poor phi/psi
 390 ASN   (  88-)  B  Poor phi/psi
 477 THR   ( 248-)  B  Poor phi/psi
 482 PRO   ( 253-)  B  Poor phi/psi
 487 GLN   ( 258-)  B  Poor phi/psi
 491 ASN   ( 262-)  B  Poor phi/psi
 497 GLU   ( 268-)  B  Poor phi/psi
 583 ARG   ( 379-)  B  Poor phi/psi
 601 ASN   ( 397-)  B  Poor phi/psi
 606 HIS   ( 405-)  B  Poor phi/psi
 607 THR   ( 406-)  B  Poor phi/psi
 662 ASP   ( 464-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.310

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 LYS   (  46-)  A      0
   4 GLU   (  47-)  A      0
  14 ASP   (  57-)  A      0
  30 ALA   (  73-)  A      0
  31 CYS   (  74-)  A      0
  34 THR   (  77-)  A      0
  35 ASP   (  78-)  A      0
  36 PRO   (  79-)  A      0
  37 ASN   (  80-)  A      0
  38 PRO   (  81-)  A      0
  41 MET   (  84-)  A      0
  45 ASN   (  88-)  A      0
  51 ASN   (  94-)  A      0
  52 MET   (  95-)  A      0
  54 LYS   (  97-)  A      0
  55 ASN   (  98-)  A      0
  72 SER   ( 115-)  A      0
  80 THR   ( 123-)  A      0
  87 GLN   ( 203-)  A      0
  89 CYS   ( 205-)  A      0
  91 LYS   ( 207-)  A      0
  94 PHE   ( 210-)  A      0
  95 ASP   ( 211-)  A      0
 105 ALA   ( 221-)  A      0
 115 LYS   ( 231-)  A      0
And so on for a total of 316 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 : 3.942

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!

  81 GLY   ( 124-)  A   3.42   28
 426 GLY   ( 124-)  B   1.59   10

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].

  96 PRO   ( 212-)  A   100.3 envelop C-beta (108 degrees)
 378 PRO   (  76-)  B   100.2 envelop C-beta (108 degrees)
 482 PRO   ( 253-)  B    22.3 half-chair N/C-delta (18 degrees)
 559 PRO   ( 354-)  B   104.1 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 157 ARG   ( 273-)  A      NH2 <->  171 HIS   ( 287-)  A      ND1    0.50    2.50  INTRA BL
 659 GLY   ( 458-)  B      N   <->  708 HOH   ( 612 )  B      O      0.37    2.33  INTRA BF
 261 HIS   ( 405-)  A      C   <->  264 ARG   ( 408-)  A      NH2    0.36    2.74  INTRA BF
 164 ASN   ( 280-)  A      ND2 <->  313 ASP   ( 457-)  A      O      0.33    2.37  INTRA BF
 606 HIS   ( 405-)  B      CG  <->  607 THR   ( 406-)  B      N      0.28    2.72  INTRA BF
 599 TYR   ( 395-)  B      CD1 <->  605 ASN   ( 404-)  B      N      0.28    2.82  INTRA BF
 606 HIS   ( 405-)  B      C   <->  609 ARG   ( 408-)  B      NH2    0.26    2.84  INTRA BF
 502 ARG   ( 273-)  B      NH2 <->  516 HIS   ( 287-)  B      ND1    0.26    2.74  INTRA BL
 312 ARG   ( 456-)  A      NH1 <->  314 GLY   ( 458-)  A      CA     0.23    2.87  INTRA BF
 583 ARG   ( 379-)  B      NH2 <->  708 HOH   ( 628 )  B      O      0.23    2.47  INTRA BL
 372 ALA   (  70-)  B      O   <->  376 CYS   (  74-)  B      N      0.22    2.48  INTRA BF
 261 HIS   ( 405-)  A      CG  <->  262 THR   ( 406-)  A      N      0.21    2.79  INTRA BL
  62 HIS   ( 105-)  A      ND1 <->  332 TRP   ( 479-)  A      CZ3    0.21    2.89  INTRA BL
 118 ASN   ( 234-)  A      ND2 <->  691 NAG   ( 501-)  A      O7     0.20    2.50  INTRA BF
 235 PHE   ( 376-)  A      C   <->  706 03G   ( 507-)  A     CL1     0.20    3.00  INTRA BL
 235 PHE   ( 376-)  A      CE1 <->  244 CYS   ( 385-)  A      SG     0.18    3.22  INTRA BL
  27 ALA   (  70-)  A      O   <->   31 CYS   (  74-)  A      N      0.18    2.52  INTRA BL
 538 ILE   ( 333-)  B      O   <->  615 ILE   ( 414-)  B      N      0.18    2.52  INTRA BL
  29 HIS   (  72-)  A      ND1 <->   30 ALA   (  73-)  A      N      0.17    2.73  INTRA BF
 407 HIS   ( 105-)  B      ND1 <->  677 TRP   ( 479-)  B      CZ3    0.17    2.93  INTRA BL
 540 GLU   ( 335-)  B      O   <->  544 ASN   ( 339-)  B      N      0.17    2.53  INTRA BF
 601 ASN   ( 397-)  B      N   <->  708 HOH   ( 636 )  B      O      0.16    2.54  INTRA BF
 254 TYR   ( 395-)  A      CD1 <->  260 ASN   ( 404-)  A      N      0.16    2.94  INTRA BF
 674 ARG   ( 476-)  B      CB  <->  678 ARG   ( 480-)  B      NH1    0.15    2.95  INTRA BL
 633 ARG   ( 432-)  B      NH2 <->  708 HOH   ( 601 )  B      O      0.15    2.55  INTRA BL
And so on for a total of 139 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.

 609 ARG   ( 408-)  B      -6.46
 600 ARG   ( 396-)  B      -6.39
 255 ARG   ( 396-)  A      -6.33
 363 TYR   (  61-)  B      -6.05
 296 GLU   ( 440-)  A      -5.85
 351 LYS   (  49-)  B      -5.84
 641 GLU   ( 440-)  B      -5.81
   6 LYS   (  49-)  A      -5.78
 264 ARG   ( 408-)  A      -5.62
 212 HIS   ( 352-)  A      -5.58
  91 LYS   ( 207-)  A      -5.53
 631 VAL   ( 430-)  B      -5.48
 286 VAL   ( 430-)  A      -5.41
 436 LYS   ( 207-)  B      -5.36
  18 TYR   (  61-)  A      -5.24
 238 ARG   ( 379-)  A      -5.20
 186 ILE   ( 326-)  A      -5.12
 531 ILE   ( 326-)  B      -5.12
 583 ARG   ( 379-)  B      -5.10
  37 ASN   (  80-)  A      -5.02
 382 ASN   (  80-)  B      -5.01

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.

 284 GLN   ( 428-)  A       286 - VAL    430- ( A)         -4.82
 629 GLN   ( 428-)  B       631 - VAL    430- ( B)         -4.84

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.

 284 GLN   ( 428-)  A   -2.78
 683 LYS   ( 485-)  B   -2.60
 673 MET   ( 475-)  B   -2.57

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

  35 ASP   (  78-)  A     -   38 PRO   (  81-)  A        -1.87
 270 ILE   ( 414-)  A     -  273 GLN   ( 417-)  A        -1.43

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: 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.

  23 HIS   (  66-)  A
  37 ASN   (  80-)  A
 100 HIS   ( 216-)  A
 113 ASN   ( 229-)  A
 130 GLN   ( 246-)  A
 188 GLN   ( 328-)  A
 407 HIS   ( 105-)  B
 432 GLN   ( 203-)  B
 445 HIS   ( 216-)  B
 458 ASN   ( 229-)  B
 475 GLN   ( 246-)  B
 544 ASN   ( 339-)  B
 623 GLN   ( 422-)  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.

   7 THR   (  50-)  A      N
  18 TYR   (  61-)  A      N
  19 GLU   (  62-)  A      N
  21 GLU   (  64-)  A      N
  23 HIS   (  66-)  A      N
  53 TRP   (  96-)  A      NE1
  83 SER   ( 199-)  A      N
 101 TYR   ( 217-)  A      OH
 118 ASN   ( 234-)  A      N
 119 GLY   ( 235-)  A      N
 131 CYS   ( 247-)  A      N
 140 SER   ( 256-)  A      N
 142 GLN   ( 258-)  A      NE2
 152 GLU   ( 268-)  A      N
 157 ARG   ( 273-)  A      NE
 157 ARG   ( 273-)  A      NH1
 158 SER   ( 274-)  A      N
 158 SER   ( 274-)  A      OG
 159 GLU   ( 275-)  A      N
 167 THR   ( 283-)  A      N
 173 ASN   ( 289-)  A      N
 174 GLU   ( 290-)  A      N
 182 ARG   ( 298-)  A      NH1
 215 SER   ( 356-)  A      N
 218 ILE   ( 359-)  A      N
And so on for a total of 80 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  62 HIS   ( 105-)  A      ND1
 195 GLU   ( 335-)  A      OE1
 229 GLU   ( 370-)  A      OE1
 233 HIS   ( 374-)  A      NE2
 261 HIS   ( 405-)  A      ND1
 487 GLN   ( 258-)  B      OE1
 578 HIS   ( 374-)  B      NE2
 606 HIS   ( 405-)  B      ND1

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.

  59 GLU   ( 102-)  A   H-bonding suggests Gln; but Alt-Rotamer
 366 GLU   (  64-)  B   H-bonding suggests Gln
 404 GLU   ( 102-)  B   H-bonding suggests Gln; but Alt-Rotamer
 680 GLU   ( 482-)  B   H-bonding suggests Gln

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 :  -1.122
  2nd generation packing quality :  -2.616
  Ramachandran plot appearance   :  -3.314 (poor)
  chi-1/chi-2 rotamer normality  :  -2.310
  Backbone conformation          :  -0.710

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.285 (tight)
  Bond angles                    :   0.430 (tight)
  Omega angle restraints         :   0.717 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.410
  B-factor distribution          :   1.511 (loose)
  Inside/Outside distribution    :   0.999

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.285 (tight)
  Bond angles                    :   0.430 (tight)
  Omega angle restraints         :   0.717 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.410
  B-factor distribution          :   1.511 (loose)
  Inside/Outside distribution    :   0.999
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.