WHAT IF Check report

This file was created 2011-12-13 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 pdb2ce2.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: X and X

All-atom RMS fit for the two chains : 1.245
CA-only RMS fit for the two chains : 0.564

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: X and X

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: C 2 2 21
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 1
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 2 1
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Error: Matthews Coefficient (Vm) too low

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.

The fact that it is lower than 1.5 in this structure might be caused by a miscalculated value of Z on the CRYST1 card.

Molecular weight of all polymer chains: 39066.305
Volume of the Unit Cell V= 306890.938
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z low: Vm= 0.982
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.100

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.

 335 GDP   ( 180-)  X  1
 336 XY2   ( 190-)  X  1
 339 XY2   ( 190-)  X  1
 340 GDP   ( 180-)  X  1

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 339 XY2   ( 190-)  X  1
 340 GDP   ( 180-)  X  1

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: X; Model number 1

Note: Ramachandran plot

Chain identifier: X; Model number 2

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

Warning: Very strange distribution of occupancy values

The distribution of the occupancy values in this file differs very much from distributions commonly observed in well-refined PDB files. This does not need to mean anything, but please look at it. This file should not be used in training sets that need to hold 'good' PDB files.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal...

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.

   1 MET   (   1-)  X    0.50
   2 THR   (   2-)  X    0.50
   3 GLU   (   3-)  X    0.50
   4 TYR   (   4-)  X    0.50
   5 LYS   (   5-)  X    0.50
   6 LEU   (   6-)  X    0.50
   7 VAL   (   7-)  X    0.50
   8 VAL   (   8-)  X    0.50
   9 VAL   (   9-)  X    0.50
  10 GLY   (  10-)  X    0.50
  11 ALA   (  11-)  X    0.50
  12 GLY   (  12-)  X    0.50
  13 GLY   (  13-)  X    0.50
  14 VAL   (  14-)  X    0.50
  15 GLY   (  15-)  X    0.50
  16 LYS   (  16-)  X    0.50
  17 SER   (  17-)  X    0.50
  18 ALA   (  18-)  X    0.50
  19 LEU   (  19-)  X    0.50
  20 THR   (  20-)  X    0.50
  21 ILE   (  21-)  X    0.50
  22 GLN   (  22-)  X    0.50
  23 LEU   (  23-)  X    0.50
  24 ILE   (  24-)  X    0.50
  25 GLN   (  25-)  X    0.50
And so on for a total of 332 lines.

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

  40 TYR   (  40-)  X
 206 TYR   (  40-)  X

Warning: Phenylalanine convention problem

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

 322 PHE   ( 156-)  X

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.

  30 ASP   (  30-)  X
  33 ASP   (  33-)  X
 108 ASP   ( 108-)  X
 196 ASP   (  30-)  X
 199 ASP   (  33-)  X
 274 ASP   ( 108-)  X
 320 ASP   ( 154-)  X

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.

   3 GLU   (   3-)  X
  31 GLU   (  31-)  X
  37 GLU   (  37-)  X
  62 GLU   (  62-)  X
  98 GLU   (  98-)  X
 169 GLU   (   3-)  X
 197 GLU   (  31-)  X
 203 GLU   (  37-)  X

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.

 246 CYS   (  80-)  X      CB   SG    1.64   -5.0

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.540
Model 2 : 0.553

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.

 198 CYS   (  32-)  X      N    CA   CB  100.92   -5.6

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 0.802
Model 2 : 0.785

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.

   3 GLU   (   3-)  X
  30 ASP   (  30-)  X
  31 GLU   (  31-)  X
  33 ASP   (  33-)  X
  37 GLU   (  37-)  X
  62 GLU   (  62-)  X
  98 GLU   (  98-)  X
 108 ASP   ( 108-)  X
 169 GLU   (   3-)  X
 196 ASP   (  30-)  X
 197 GLU   (  31-)  X
 199 ASP   (  33-)  X
 203 GLU   (  37-)  X
 274 ASP   ( 108-)  X
 320 ASP   ( 154-)  X

Torsion-related checks

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -0.238
Model 2 : -1.519

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.

  63 GLU   (  63-)  X    -2.4
 228 GLU   (  62-)  X    -2.1
 210 VAL   (  44-)  X    -2.1
 192 ASN   (  26-)  X    -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.

  54 ASP   (  54-)  X  omega poor
  59 ALA   (  59-)  X  omega poor
  60 GLY   (  60-)  X  omega poor
  62 GLU   (  62-)  X  omega poor
  63 GLU   (  63-)  X  Poor phi/psi, omega poor
  80 CYS   (  80-)  X  omega poor
 117 LYS   ( 117-)  X  Poor phi/psi
 144 THR   ( 144-)  X  omega poor
 149 ARG   ( 149-)  X  Poor phi/psi
 181 GLY   (  15-)  X  Poor phi/psi
 192 ASN   (  26-)  X  Poor phi/psi
 213 ASP   (  47-)  X  Poor phi/psi
 226 GLY   (  60-)  X  omega poor
 227 GLN   (  61-)  X  Poor phi/psi
 228 GLU   (  62-)  X  Poor phi/psi
 229 GLU   (  63-)  X  Poor phi/psi
 241 GLY   (  75-)  X  Poor phi/psi
 244 PHE   (  78-)  X  omega poor
 283 LYS   ( 117-)  X  Poor phi/psi
 288 ALA   ( 122-)  X  Poor phi/psi
 315 ARG   ( 149-)  X  Poor phi/psi
 331 GLN   ( 165-)  X  omega poor
 chi-1/chi-2 correlation Z-score : -1.689

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -2.144
Model 2 : -1.235

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 183 SER   (  17-)  X    0.33
 112 VAL   ( 112-)  X    0.35
 302 SER   ( 136-)  X    0.36
 136 SER   ( 136-)  X    0.39
  17 SER   (  17-)  X    0.40

Warning: Unusual backbone conformations

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

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

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

   9 VAL   (   9-)  X      0
  11 ALA   (  11-)  X      0
  14 VAL   (  14-)  X      0
  25 GLN   (  25-)  X      0
  31 GLU   (  31-)  X      0
  32 CYS   (  32-)  X      0
  38 ASP   (  38-)  X      0
  50 THR   (  50-)  X      0
  51 CYS   (  51-)  X      0
  61 GLN   (  61-)  X      0
  63 GLU   (  63-)  X      0
  64 TYR   (  64-)  X      0
 107 ASP   ( 107-)  X      0
 108 ASP   ( 108-)  X      0
 110 PRO   ( 110-)  X      0
 116 ASN   ( 116-)  X      0
 117 LYS   ( 117-)  X      0
 118 SER   ( 118-)  X      0
 120 LEU   ( 120-)  X      0
 121 ALA   ( 121-)  X      0
 122 ALA   ( 122-)  X      0
 123 ARG   ( 123-)  X      0
 126 GLU   ( 126-)  X      0
 137 TYR   ( 137-)  X      0
 149 ARG   ( 149-)  X      0
And so on for a total of 107 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.154

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 8.069
Model 2 : 6.125

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

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).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

  32 CYS   (  32-)  X    A SG  <->  337 XY2   ( 190-)  X      C19    1.56    1.84
  20 THR   (  20-)  X    A CG2 <->  337 XY2   ( 190-)  X      O9     0.75    2.05
  25 GLN   (  25-)  X    A NE2 <->  337 XY2   ( 190-)  X      N5     0.44    2.56
  25 GLN   (  25-)  X    A NE2 <->  337 XY2   ( 190-)  X      O6     0.39    2.31
  32 CYS   (  32-)  X    A SG  <->  337 XY2   ( 190-)  X      C17    0.27    3.13
  32 CYS   (  32-)  X    A SG  <->  337 XY2   ( 190-)  X      C16    0.24    3.16
  40 TYR   (  40-)  X    A CD2 <->  337 XY2   ( 190-)  X      O9     0.08    2.72
  20 THR   (  20-)  X    A CG2 <->  337 XY2   ( 190-)  X      N8     0.07    3.03
  32 CYS   (  32-)  X    A CB  <->  337 XY2   ( 190-)  X      C19    0.06    3.14
 116 ASN   ( 116-)  X    A ND2 <->  338 GDP   ( 180-)  X      N7     0.03    2.97

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck


Note: Inside/Outside RMS Z-score plot

Chain identifier: X; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: X; Model number 2

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Note: Quality value plot

Chain identifier: X; Model number 1

Note: Quality value plot

Chain identifier: X; Model number 2

Warning: Low packing Z-score for some residues


Warning: Abnormal packing Z-score for sequential residues


Note: Per-model averages for NQA


Note: Second generation quality Z-score plot

Chain identifier: X; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: X; Model number 2

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms


Warning: Water molecules need moving


Error: Water molecules without hydrogen bonds


Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: Unusual ion packing


Warning: Unusual water packing


Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure







Note: Summary report for depositors of a structure