WHAT IF Check report

This file was created 2011-12-16 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 pdb1mf8.ent

Checks that need to be done early-on in validation

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.

 692 DAL   (   1-)  D  -
 693 MVA   (   4-)  D  -
 694 BMT   (   5-)  D  -
 695 ABA   (   6-)  D  -
 696 SAR   (   7-)  D  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 681 MLE   (   2-)  D  -   N   bound to  692 DAL   (   1-)  D  -   C

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   7 SER   (  26-)  A  -   OG
  13 LYS   (  32-)  A  -   CE
  13 LYS   (  32-)  A  -   NZ
  57 LYS   (  76-)  A  -   CE
  57 LYS   (  76-)  A  -   NZ
  91 ASN   ( 110-)  A  -   OD1
  91 ASN   ( 110-)  A  -   ND2
 139 GLU   ( 158-)  A  -   CG
 139 GLU   ( 158-)  A  -   CD
 139 GLU   ( 158-)  A  -   OE1
 139 GLU   ( 158-)  A  -   OE2
 214 SER   ( 233-)  A  -   OG
 218 GLU   ( 237-)  A  -   CD
 218 GLU   ( 237-)  A  -   OE1
 218 GLU   ( 237-)  A  -   OE2
 224 LYS   ( 243-)  A  -   CG
 224 LYS   ( 243-)  A  -   CD
 224 LYS   ( 243-)  A  -   CE
 224 LYS   ( 243-)  A  -   NZ
 226 GLN   ( 245-)  A  -   CG
 226 GLN   ( 245-)  A  -   CD
 226 GLN   ( 245-)  A  -   OE1
 226 GLN   ( 245-)  A  -   NE2
 233 THR   ( 252-)  A  -   OG1
 276 GLN   ( 295-)  A  -   CG
And so on for a total of 69 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 681 MLE   (   2-)  D
 682 MLE   (   3-)  D
 683 MLE   (   8-)  D
 685 MLE   (  10-)  D

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 ALA   (  20-)  A    High
   2 VAL   (  21-)  A    High
   3 PRO   (  22-)  A    High
   4 PHE   (  23-)  A    High
   5 PRO   (  24-)  A    High
   6 PRO   (  25-)  A    High
   7 SER   (  26-)  A    High
   8 HIS   (  27-)  A    High
   9 ARG   (  28-)  A    High
  10 LEU   (  29-)  A    High
  11 THR   (  30-)  A    High
  12 ALA   (  31-)  A    High
  13 LYS   (  32-)  A    High
  14 GLU   (  33-)  A    High
  15 VAL   (  34-)  A    High
  16 PHE   (  35-)  A    High
  17 ASP   (  36-)  A    High
  18 ASN   (  37-)  A    High
  19 ASP   (  38-)  A    High
  20 GLY   (  39-)  A    High
  21 LYS   (  40-)  A    High
  22 PRO   (  41-)  A    High
  23 ARG   (  42-)  A    High
  24 VAL   (  43-)  A    High
  25 ASP   (  44-)  A    High
And so on for a total of 310 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. 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

Note: B-factor plot

Chain identifier: C

Nomenclature related problems

Warning: Tyrosine convention problem

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

 239 TYR   ( 258-)  A
 269 TYR   ( 288-)  A

Warning: Phenylalanine convention problem

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

 229 PHE   ( 248-)  A
 240 PHE   ( 259-)  A
 327 PHE   ( 346-)  A
 374 PHE   (  26-)  B
 538 PHE   (  22-)  C

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  17 ASP   (  36-)  A
 676 ASP   ( 160-)  C

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.

  34 GLU   (  53-)  A

Geometric checks

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.

  17 ASP   (  36-)  A
  34 GLU   (  53-)  A
 676 ASP   ( 160-)  C

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.

 330 VAL   ( 349-)  A    5.71
  24 VAL   (  43-)  A    5.13
 334 SER   ( 353-)  A    4.88
 439 LEU   (  91-)  B    4.87
 480 VAL   ( 132-)  B    4.26
 645 PHE   ( 129-)  C    4.22
  51 SER   (  70-)  A    4.03
 504 VAL   ( 156-)  B    4.00

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.550

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 : -3.660

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.

  73 HIS   (  92-)  A    -3.1
  27 LEU   (  46-)  A    -2.8
 103 ARG   ( 122-)  A    -2.4
 577 MET   (  61-)  C    -2.4
 327 PHE   ( 346-)  A    -2.3
 413 GLY   (  65-)  B    -2.3
 471 LEU   ( 123-)  B    -2.2
 256 LEU   ( 275-)  A    -2.2
 323 TRP   ( 342-)  A    -2.2
  26 ILE   (  45-)  A    -2.2
 260 ARG   ( 279-)  A    -2.2
  92 THR   ( 111-)  A    -2.2
  59 LEU   (  78-)  A    -2.2
 354 TYR   (   6-)  B    -2.1
 398 GLN   (  50-)  B    -2.1
 484 ILE   ( 136-)  B    -2.1
 310 MET   ( 329-)  A    -2.1
 124 THR   ( 143-)  A    -2.1
 650 GLU   ( 134-)  C    -2.0
 238 SER   ( 257-)  A    -2.0
 100 TYR   ( 119-)  A    -2.0
 602 GLU   (  86-)  C    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  34 GLU   (  53-)  A  Poor phi/psi
  64 ALA   (  83-)  A  PRO omega poor
  75 GLN   (  94-)  A  Poor phi/psi
  99 ASP   ( 118-)  A  Poor phi/psi
 102 ASP   ( 121-)  A  Poor phi/psi
 103 ARG   ( 122-)  A  Poor phi/psi
 151 TYR   ( 170-)  A  Poor phi/psi
 174 GLN   ( 193-)  A  Poor phi/psi
 228 HIS   ( 247-)  A  Poor phi/psi
 238 SER   ( 257-)  A  Poor phi/psi
 261 ALA   ( 280-)  A  Poor phi/psi
 262 HIS   ( 281-)  A  Poor phi/psi
 269 TYR   ( 288-)  A  Poor phi/psi
 293 LEU   ( 312-)  A  Poor phi/psi
 294 ASP   ( 313-)  A  Poor phi/psi
 295 VAL   ( 314-)  A  Poor phi/psi
 354 TYR   (   6-)  B  Poor phi/psi
 413 GLY   (  65-)  B  Poor phi/psi
 508 ASP   ( 160-)  B  Poor phi/psi
 529 ASP   (  13-)  C  Poor phi/psi
 576 PHE   (  60-)  C  Poor phi/psi
 586 HIS   (  70-)  C  Poor phi/psi
 587 ASN   (  71-)  C  Poor phi/psi
 602 GLU   (  86-)  C  Poor phi/psi
 622 ASN   ( 106-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.520

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.520

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!

  15 VAL   (  34-)  A      0
  16 PHE   (  35-)  A      0
  23 ARG   (  42-)  A      0
  33 LYS   (  52-)  A      0
  34 GLU   (  53-)  A      0
  37 LEU   (  56-)  A      0
  63 ASP   (  82-)  A      0
  64 ALA   (  83-)  A      0
  71 ASP   (  90-)  A      0
  73 HIS   (  92-)  A      0
  75 GLN   (  94-)  A      0
  91 ASN   ( 110-)  A      0
  97 LEU   ( 116-)  A      0
  99 ASP   ( 118-)  A      0
 100 TYR   ( 119-)  A      0
 102 ASP   ( 121-)  A      0
 103 ARG   ( 122-)  A      0
 105 TYR   ( 124-)  A      0
 121 TYR   ( 140-)  A      0
 124 THR   ( 143-)  A      0
 132 HIS   ( 151-)  A      0
 133 GLU   ( 152-)  A      0
 134 CYS   ( 153-)  A      0
 140 TYR   ( 159-)  A      0
 142 THR   ( 161-)  A      0
And so on for a total of 270 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 : 1.401

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].

 325 PRO   ( 344-)  A   105.0 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.

 686 ALA   (  11-)  D      C   <->  692 DAL   (   1-)  D      N      1.37    1.33  INTRA BL
 693 MVA   (   4-)  D      C   <->  694 BMT   (   5-)  D      N      1.36    1.34  INTRA BL
 695 ABA   (   6-)  D      C   <->  696 SAR   (   7-)  D      N      1.36    1.34  INTRA BL
 694 BMT   (   5-)  D      C   <->  695 ABA   (   6-)  D      N      1.36    1.34  INTRA BL
 683 MLE   (   8-)  D      N   <->  696 SAR   (   7-)  D      C      1.36    1.34  INTRA BL
 681 MLE   (   2-)  D      N   <->  692 DAL   (   1-)  D      C      1.35    1.35  INTRA BL
 682 MLE   (   3-)  D      C   <->  693 MVA   (   4-)  D      N      1.34    1.36  INTRA BL
 683 MLE   (   8-)  D      CA  <->  696 SAR   (   7-)  D      C      0.80    2.40  INTRA BL
 681 MLE   (   2-)  D      CN  <->  692 DAL   (   1-)  D      C      0.78    2.42  INTRA BL
 681 MLE   (   2-)  D      CA  <->  692 DAL   (   1-)  D      C      0.77    2.43  INTRA BL
 683 MLE   (   8-)  D      CN  <->  696 SAR   (   7-)  D      C      0.77    2.43  INTRA BL
 303 LEU   ( 322-)  A      CD2 <->  310 MET   ( 329-)  A      SD     0.74    2.66  INTRA BF
 686 ALA   (  11-)  D      CA  <->  692 DAL   (   1-)  D      N      0.69    2.41  INTRA BL
 694 BMT   (   5-)  D      CA  <->  695 ABA   (   6-)  D      N      0.68    2.42  INTRA BL
 693 MVA   (   4-)  D      CA  <->  694 BMT   (   5-)  D      N      0.63    2.47  INTRA BL
 682 MLE   (   3-)  D      CA  <->  693 MVA   (   4-)  D      N      0.63    2.47  INTRA BL
 232 ASN   ( 251-)  A      ND2 <->  240 PHE   ( 259-)  A      CE1    0.61    2.49  INTRA BF
 551 ASN   (  35-)  C      O   <->  555 LEU   (  39-)  C      CG     0.56    2.24  INTRA BF
 695 ABA   (   6-)  D      CA  <->  696 SAR   (   7-)  D      N      0.51    2.49  INTRA BL
 232 ASN   ( 251-)  A      OD1 <->  235 ARG   ( 254-)  A      N      0.47    2.23  INTRA BF
 131 ASN   ( 150-)  A      ND2 <->  212 LEU   ( 231-)  A      O      0.47    2.23  INTRA BF
 545 VAL   (  29-)  C      CG1 <->  603 ASN   (  87-)  C      ND2    0.46    2.64  INTRA BF
 682 MLE   (   3-)  D      CA  <->  693 MVA   (   4-)  D      CN     0.46    2.74  INTRA BL
 693 MVA   (   4-)  D      CA  <->  694 BMT   (   5-)  D      CN     0.45    2.75  INTRA BL
 693 MVA   (   4-)  D      O   <->  694 BMT   (   5-)  D      N      0.45    2.25  INTRA BL
And so on for a total of 273 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 205 TYR   ( 224-)  A      -8.46
 354 TYR   (   6-)  B      -7.31
   4 PHE   (  23-)  A      -6.64
 224 LYS   ( 243-)  A      -6.02
 660 ARG   ( 144-)  C      -5.97
 398 GLN   (  50-)  B      -5.75
 664 ARG   ( 148-)  C      -5.71
  55 GLN   (  74-)  A      -5.64
  18 ASN   (  37-)  A      -5.34
 213 TRP   ( 232-)  A      -5.34
 518 VAL   (   2-)  C      -5.32
 586 HIS   (  70-)  C      -5.26
 123 LYS   ( 142-)  A      -5.18
 322 TYR   ( 341-)  A      -5.17
 326 ASN   ( 345-)  A      -5.11
 357 GLU   (   9-)  B      -5.11
 200 LYS   ( 219-)  A      -5.03

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.

 199 PHE   ( 218-)  A       201 - GLU    220- ( A)         -4.88

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

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.

 293 LEU   ( 312-)  A   -3.01

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

  73 HIS   (  92-)  A
  91 ASN   ( 110-)  A
 228 HIS   ( 247-)  A
 252 HIS   ( 271-)  A

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.

  25 ASP   (  44-)  A      N
  34 GLU   (  53-)  A      N
 101 VAL   ( 120-)  A      N
 115 TRP   ( 134-)  A      NE1
 126 PHE   ( 145-)  A      N
 127 LEU   ( 146-)  A      N
 129 ARG   ( 148-)  A      NH1
 131 ASN   ( 150-)  A      N
 131 ASN   ( 150-)  A      ND2
 134 CYS   ( 153-)  A      N
 140 TYR   ( 159-)  A      N
 152 SER   ( 171-)  A      N
 180 HIS   ( 199-)  A      N
 183 LEU   ( 202-)  A      N
 184 SER   ( 203-)  A      N
 184 SER   ( 203-)  A      OG
 198 ARG   ( 217-)  A      N
 198 ARG   ( 217-)  A      NE
 206 GLY   ( 225-)  A      N
 209 CYS   ( 228-)  A      N
 219 ASP   ( 238-)  A      N
 221 GLY   ( 240-)  A      N
 225 THR   ( 244-)  A      N
 232 ASN   ( 251-)  A      ND2
 237 CYS   ( 256-)  A      N
And so on for a total of 64 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.

  56 GLU   (  75-)  A      OE1
 262 HIS   ( 281-)  A      NE2
 320 HIS   ( 339-)  A      ND1
 357 GLU   (   9-)  B      OE1
 624 ASN   ( 108-)  C      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 687  CA   ( 401-)  B   -.-  -.-  Low probability ion. B= 91.3
 689  CA   ( 403-)  B     0.81   1.03 Scores about as good as NA
 690  CA   ( 404-)  B   -.-  -.-  Low probability ion. B= 91.5
Since there are no waters, the water check has been skipped.

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.

  17 ASP   (  36-)  A   H-bonding suggests Asn
 133 GLU   ( 152-)  A   H-bonding suggests Gln
 157 ASP   ( 176-)  A   H-bonding suggests Asn; but Alt-Rotamer
 210 ASP   ( 229-)  A   H-bonding suggests Asn; but Alt-Rotamer
 227 GLU   ( 246-)  A   H-bonding suggests Gln
 340 GLU   ( 359-)  A   H-bonding suggests Gln
 481 ASP   ( 133-)  B   H-bonding suggests Asn
 597 GLU   (  81-)  C   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 :  -0.937
  2nd generation packing quality :  -1.135
  Ramachandran plot appearance   :  -3.660 (poor)
  chi-1/chi-2 rotamer normality  :  -3.520 (poor)
  Backbone conformation          :  -0.714

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.417 (tight)
  Bond angles                    :   0.695
  Omega angle restraints         :   0.255 (tight)
  Side chain planarity           :   0.293 (tight)
  Improper dihedral distribution :   0.652
  B-factor distribution          :   0.944
  Inside/Outside distribution    :   0.985

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 : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.417 (tight)
  Bond angles                    :   0.695
  Omega angle restraints         :   0.255 (tight)
  Side chain planarity           :   0.293 (tight)
  Improper dihedral distribution :   0.652
  B-factor distribution          :   0.944
  Inside/Outside distribution    :   0.985
==============

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.