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 pdb3l2m.ent

Checks that need to be done early-on in validation

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: 55442.055
Volume of the Unit Cell V= 964604.938
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.350
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.350

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 466 LYS   ( 466-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 466 LYS   ( 466-)  A  -

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.

 497 GLC   ( 601-)  A  -   O4  bound to  498 GLC   ( 606-)  A  -   C1
 498 GLC   ( 606-)  A  -   O4  bound to  499 GLC   ( 605-)  A  -   C1
 499 GLC   ( 605-)  A  -   O4  bound to  500 GLC   ( 604-)  A  -   C1
 500 GLC   ( 604-)  A  -   O4  bound to  501 GLC   ( 603-)  A  -   C1
 501 GLC   ( 603-)  A  -   O4  bound to  502 GLC   ( 602-)  A  -   C1
 502 GLC   ( 602-)  A  -   O4  bound to  497 GLC   ( 601-)  A  -   C1
 503 GLC   ( 706-)  A  -   O4  bound to  504 GLC   ( 705-)  A  -   C1
 504 GLC   ( 705-)  A  -   O4  bound to  505 GLC   ( 704-)  A  -   C1
 505 GLC   ( 704-)  A  -   O4  bound to  506 GLC   ( 703-)  A  -   C1
 506 GLC   ( 703-)  A  -   O4  bound to  507 GLC   ( 702-)  A  -   C1
 507 GLC   ( 702-)  A  -   O4  bound to  508 GLC   ( 701-)  A  -   C1
 508 GLC   ( 701-)  A  -   O4  bound to  503 GLC   ( 706-)  A  -   C1
 509 GLC   ( 803-)  A  -   O4  bound to  510 GLC   ( 802-)  A  -   C1
 510 GLC   ( 802-)  A  -   O4  bound to  511 GLC   ( 801-)  A  -   C1
 511 GLC   ( 801-)  A  -   O4  bound to  512 GLC   ( 806-)  A  -   C1
 512 GLC   ( 806-)  A  -   O4  bound to  513 GLC   ( 805-)  A  -   C1
 513 GLC   ( 805-)  A  -   O4  bound to  514 GLC   ( 804-)  A  -   C1
 514 GLC   ( 804-)  A  -   O4  bound to  509 GLC   ( 803-)  A  -   C1

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.

 503 GLC   ( 706-)  A    High
 504 GLC   ( 705-)  A    High
 505 GLC   ( 704-)  A    High
 506 GLC   ( 703-)  A    High
 509 GLC   ( 803-)  A    High
 510 GLC   ( 802-)  A    High
 511 GLC   ( 801-)  A    High
 512 GLC   ( 806-)  A    High
 513 GLC   ( 805-)  A    High
 514 GLC   ( 804-)  A    High

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

 438 SER   ( 438-)  A    0.70
 461 SER   ( 461-)  A    0.70
 471 SER   ( 471-)  A    0.70
 495 LYS   ( 495-)  A    0.70

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: 21

Crystal temperature (K) :298.000

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  30 ARG   (  30-)  A
  61 ARG   (  61-)  A
  85 ARG   (  85-)  A
  92 ARG   (  92-)  A
 124 ARG   ( 124-)  A
 158 ARG   ( 158-)  A
 176 ARG   ( 176-)  A
 227 ARG   ( 227-)  A
 252 ARG   ( 252-)  A
 267 ARG   ( 267-)  A
 291 ARG   ( 291-)  A
 319 ARG   ( 319-)  A
 389 ARG   ( 389-)  A
 398 ARG   ( 398-)  A
 421 ARG   ( 421-)  A

Warning: Tyrosine convention problem

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

   2 TYR   (   2-)  A
  62 TYR   (  62-)  A
  94 TYR   (  94-)  A
 131 TYR   ( 131-)  A
 342 TYR   ( 342-)  A
 449 TYR   ( 449-)  A

Warning: Phenylalanine convention problem

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

  37 PHE   (  37-)  A
 136 PHE   ( 136-)  A
 222 PHE   ( 222-)  A
 229 PHE   ( 229-)  A
 256 PHE   ( 256-)  A
 286 PHE   ( 286-)  A
 295 PHE   ( 295-)  A
 477 PHE   ( 477-)  A

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.

  23 ASP   (  23-)  A
  96 ASP   (  96-)  A
 138 ASP   ( 138-)  A
 159 ASP   ( 159-)  A
 173 ASP   ( 173-)  A
 181 ASP   ( 181-)  A
 188 ASP   ( 188-)  A
 206 ASP   ( 206-)  A
 236 ASP   ( 236-)  A
 297 ASP   ( 297-)  A
 300 ASP   ( 300-)  A
 353 ASP   ( 353-)  A
 381 ASP   ( 381-)  A
 402 ASP   ( 402-)  A
 432 ASP   ( 432-)  A
 451 ASP   ( 451-)  A
 456 ASP   ( 456-)  A
 485 ASP   ( 485-)  A

Warning: Glutamic acid convention problem

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

  18 GLU   (  18-)  A
  29 GLU   (  29-)  A
  76 GLU   (  76-)  A
 149 GLU   ( 149-)  A
 233 GLU   ( 233-)  A
 246 GLU   ( 246-)  A
 272 GLU   ( 272-)  A
 282 GLU   ( 282-)  A
 369 GLU   ( 369-)  A
 493 GLU   ( 493-)  A

Geometric checks

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.525
RMS-deviation in bond distances: 0.012

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.

  15 HIS   (  15-)  A      CG   ND1  CE1 109.69    4.1

Error: Nomenclature error(s)

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

  18 GLU   (  18-)  A
  23 ASP   (  23-)  A
  29 GLU   (  29-)  A
  30 ARG   (  30-)  A
  61 ARG   (  61-)  A
  76 GLU   (  76-)  A
  85 ARG   (  85-)  A
  92 ARG   (  92-)  A
  96 ASP   (  96-)  A
 124 ARG   ( 124-)  A
 138 ASP   ( 138-)  A
 149 GLU   ( 149-)  A
 158 ARG   ( 158-)  A
 159 ASP   ( 159-)  A
 173 ASP   ( 173-)  A
 176 ARG   ( 176-)  A
 181 ASP   ( 181-)  A
 188 ASP   ( 188-)  A
 206 ASP   ( 206-)  A
 227 ARG   ( 227-)  A
 233 GLU   ( 233-)  A
 236 ASP   ( 236-)  A
 246 GLU   ( 246-)  A
 252 ARG   ( 252-)  A
 267 ARG   ( 267-)  A
 272 GLU   ( 272-)  A
 282 GLU   ( 282-)  A
 291 ARG   ( 291-)  A
 297 ASP   ( 297-)  A
 300 ASP   ( 300-)  A
 319 ARG   ( 319-)  A
 353 ASP   ( 353-)  A
 369 GLU   ( 369-)  A
 381 ASP   ( 381-)  A
 389 ARG   ( 389-)  A
 398 ARG   ( 398-)  A
 402 ASP   ( 402-)  A
 421 ARG   ( 421-)  A
 432 ASP   ( 432-)  A
 451 ASP   ( 451-)  A
 456 ASP   ( 456-)  A
 485 ASP   ( 485-)  A
 493 GLU   ( 493-)  A

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.

 376 THR   ( 376-)  A    -3.0
  45 PRO   (  45-)  A    -2.5
 163 VAL   ( 163-)  A    -2.3
  56 ARG   (  56-)  A    -2.2
 486 PRO   ( 486-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   5 GLN   (   5-)  A  Poor phi/psi
  10 ARG   (  10-)  A  omega poor
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
  56 ARG   (  56-)  A  Poor phi/psi
 102 MET   ( 102-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 194 PHE   ( 194-)  A  omega poor
 198 ALA   ( 198-)  A  Poor phi/psi
 215 HIS   ( 215-)  A  omega poor
 221 TRP   ( 221-)  A  Poor phi/psi
 268 LYS   ( 268-)  A  Poor phi/psi
 270 SER   ( 270-)  A  Poor phi/psi
 292 ALA   ( 292-)  A  omega poor
 303 ARG   ( 303-)  A  omega poor
 317 ASP   ( 317-)  A  omega poor
 340 SER   ( 340-)  A  omega poor
 341 SER   ( 341-)  A  omega poor
 350 ASN   ( 350-)  A  Poor phi/psi
 362 ASN   ( 362-)  A  omega poor
 376 THR   ( 376-)  A  Poor phi/psi
 380 ASN   ( 380-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 408 ASN   ( 408-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 456 ASP   ( 456-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -0.977

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!

   5 GLN   (   5-)  A      0
   8 SER   (   8-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  30 ARG   (  30-)  A      0
  31 TYR   (  31-)  A      0
  32 LEU   (  32-)  A      0
  45 PRO   (  45-)  A      0
  48 ASN   (  48-)  A      0
  52 THR   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 SER   (  55-)  A      0
  56 ARG   (  56-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
  73 SER   (  73-)  A      0
  75 ASN   (  75-)  A      0
And so on for a total of 229 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 228 PRO   ( 228-)  A    0.04 LOW
 361 PRO   ( 361-)  A    0.19 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  54 PRO   (  54-)  A   -61.1 half-chair C-beta/C-alpha (-54 degrees)
 127 PRO   ( 127-)  A  -112.0 envelop C-gamma (-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.

 317 ASP   ( 317-)  A    A OD2 <->  518 HOH   ( 761 )  A    B O      0.90    1.50  INTRA BL
  77 ASN   (  77-)  A      ND2 <->  518 HOH   ( 647 )  A      O      0.45    2.25  INTRA
 317 ASP   ( 317-)  A    A CG  <->  518 HOH   ( 761 )  A    B O      0.23    2.57  INTRA BL
 470 SER   ( 470-)  A    A OG  <->  472 ASP   ( 472-)  A      OD1    0.23    2.17  INTRA
 505 GLC   ( 704-)  A      O3  <->  506 GLC   ( 703-)  A      O2     0.22    2.08  INTRA BF
 261 LYS   ( 261-)  A    A NZ  <->  518 HOH   ( 915 )  A      O      0.20    2.50  INTRA
 135 ASP   ( 135-)  A      OD2 <->  513 GLC   ( 805-)  A      C6     0.19    2.61  INTRA BF
 305 HIS   ( 305-)  A      NE2 <->  356 ASP   ( 356-)  A      OD2    0.19    2.51  INTRA BF
 424 ARG   ( 424-)  A    A NH1 <->  518 HOH   (1060 )  A      O      0.17    2.53  INTRA
 503 GLC   ( 706-)  A      O2  <->  508 GLC   ( 701-)  A      O3     0.17    2.23  INTRA BF
 124 ARG   ( 124-)  A      NH2 <->  138 ASP   ( 138-)  A    A OD2    0.13    2.57  INTRA
 185 LYS   ( 185-)  A    A NZ  <->  518 HOH   (1021 )  A      O      0.12    2.58  INTRA
 392 ARG   ( 392-)  A    A NH1 <->  393 ASN   ( 393-)  A      OD1    0.11    2.59  INTRA BL
 135 ASP   ( 135-)  A      OD2 <->  513 GLC   ( 805-)  A      O6     0.11    2.29  INTRA BF
 424 ARG   ( 424-)  A    A NH2 <->  518 HOH   (1079 )  A      O      0.09    2.61  INTRA
 173 ASP   ( 173-)  A    A OD1 <->  518 HOH   ( 737 )  A    A O      0.09    2.31  INTRA BL
 201 HIS   ( 201-)  A      NE2 <->  518 HOH   (1008 )  A      O      0.08    2.62  INTRA
 352 GLN   ( 352-)  A      OE1 <->  518 HOH   (1089 )  A      O      0.05    2.35  INTRA BF
 437 SER   ( 437-)  A      N   <->  518 HOH   ( 753 )  A      O      0.05    2.65  INTRA
  15 HIS   (  15-)  A      CD2 <->  518 HOH   ( 765 )  A      O      0.04    2.76  INTRA BL
 355 ASN   ( 355-)  A      OD1 <->  518 HOH   (1033 )  A      O      0.04    2.36  INTRA
 356 ASP   ( 356-)  A      OD1 <->  518 HOH   (1045 )  A      O      0.04    2.36  INTRA
 507 GLC   ( 702-)  A      O3  <->  508 GLC   ( 701-)  A      O2     0.03    2.27  INTRA BF
 216 ASN   ( 216-)  A      OD1 <->  227 ARG   ( 227-)  A      NH1    0.03    2.67  INTRA
 348 PHE   ( 348-)  A      N   <->  518 HOH   ( 929 )  A      O      0.03    2.67  INTRA
 240 GLU   ( 240-)  A    A OE1 <->  518 HOH   ( 992 )  A    A O      0.02    2.38  INTRA
 100 ASN   ( 100-)  A      ND2 <->  101 HIS   ( 101-)  A      ND1    0.01    2.99  INTRA BL
 402 ASP   ( 402-)  A      O   <->  518 HOH   (1054 )  A      O      0.01    2.39  INTRA
 368 LYS   ( 368-)  A      NZ  <->  518 HOH   ( 576 )  A      O      0.01    2.69  INTRA
 373 ASN   ( 373-)  A      N   <->  377 THR   ( 377-)  A      O      0.01    2.69  INTRA BL

Packing, accessibility and threading

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.

  72 ARG   (  72-)  A      -7.15
 118 TYR   ( 118-)  A      -5.93
   2 TYR   (   2-)  A      -5.63
  53 ASN   (  53-)  A      -5.46
 343 ARG   ( 343-)  A      -5.44
 237 LEU   ( 237-)  A      -5.42
 284 TRP   ( 284-)  A      -5.35
 279 ASN   ( 279-)  A      -5.35
 303 ARG   ( 303-)  A      -5.33
  88 ASN   (  88-)  A      -5.31
 123 ASN   ( 123-)  A      -5.30
 305 HIS   ( 305-)  A      -5.30
 302 GLN   ( 302-)  A      -5.29
  30 ARG   (  30-)  A      -5.29
   7 GLN   (   7-)  A      -5.12

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.

  53 ASN   (  53-)  A   -3.72
 163 VAL   ( 163-)  A   -2.63
 276 TYR   ( 276-)  A   -2.62
  17 PHE   (  17-)  A   -2.53
 148 ILE   ( 148-)  A   -2.51

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.

 518 HOH   ( 534 )  A      O     52.22   24.70   56.08
 518 HOH   ( 859 )  A      O     42.92   56.58   41.33
 518 HOH   ( 923 )  A      O     54.23   35.90   65.30

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.

 347 ASN   ( 347-)  A
 435 GLN   ( 435-)  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.

  59 TRP   (  59-)  A      N
  87 ASN   (  87-)  A      ND2
 101 HIS   ( 101-)  A      N
 134 TRP   ( 134-)  A      NE1
 151 TYR   ( 151-)  A      N
 193 GLY   ( 193-)  A      N
 251 GLY   ( 251-)  A      N
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 316 TRP   ( 316-)  A      NE1
 344 TRP   ( 344-)  A      N
 352 GLN   ( 352-)  A      N
 434 TRP   ( 434-)  A      N
 505 GLC   ( 704-)  A      O6
Only metal coordination for  100 ASN  ( 100-) A      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.

  15 HIS   (  15-)  A      NE2

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+.

 516  CA   ( 501-)  A     0.76   1.00 Scores about as good as NA

Warning: Unusual water packing

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

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

 518 HOH   ( 732 )  A      O  1.11  K  4
 518 HOH   ( 776 )  A      O  0.86  K  4
 518 HOH   ( 787 )  A      O  0.95  K  4
 518 HOH   ( 842 )  A      O  1.14  K  5
 518 HOH   ( 843 )  A      O  0.98  K  5 Ion-B
 518 HOH   ( 881 )  A      O  0.91  K  4 Ion-B

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.

 181 ASP   ( 181-)  A   H-bonding suggests Asn
 300 ASP   ( 300-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.160
  2nd generation packing quality :  -2.112
  Ramachandran plot appearance   :  -0.666
  chi-1/chi-2 rotamer normality  :  -0.977
  Backbone conformation          :  -0.928

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.525 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   1.082
  Side chain planarity           :   0.693
  Improper dihedral distribution :   0.806
  B-factor distribution          :   1.265
  Inside/Outside distribution    :   1.007

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.97


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.525 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   1.082
  Side chain planarity           :   0.693
  Improper dihedral distribution :   0.806
  B-factor distribution          :   1.265
  Inside/Outside distribution    :   1.007
==============

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.