WHAT IF Check report

This file was created 2012-01-25 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 pdb2f24.ent

Checks that need to be done early-on in validation

Warning: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

 361 HOH   (1075 )  A      O
 361 HOH   (1082 )  A      O
 361 HOH   (1191 )  A      O
 361 HOH   (1219 )  A      O

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

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

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.

 307 VAL   ( 325-)  A    0.50

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

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

 171 TYR   ( 179-)  A
 277 TYR   ( 295-)  A
 292 TYR   ( 310-)  A
 336 TYR   ( 354-)  A

Warning: Phenylalanine convention problem

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

  91 PHE   (  99-)  A
  94 PHE   ( 102-)  A
 149 PHE   ( 157-)  A
 187 PHE   ( 195-)  A
 267 PHE   ( 279-)  A
 349 PHE   ( 367-)  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.

 207 ASP   ( 215-)  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.

  64 GLU   (  72-)  A
 254 GLU   ( 266-)  A
 343 GLU   ( 361-)  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: 0.259
RMS-deviation in bond distances: 0.006

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.

 189 PHE   ( 197-)  A      N    CA   C    99.92   -4.0

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). 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 angles: 0.657
RMS-deviation in bond angles: 1.464

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.

  64 GLU   (  72-)  A
 207 ASP   ( 215-)  A
 254 GLU   ( 266-)  A
 343 GLU   ( 361-)  A

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.

 189 PHE   ( 197-)  A    4.21
 224 ALA   ( 236-)  A    4.09

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.

 298 PRO   ( 316-)  A    -3.0
 148 THR   ( 156-)  A    -2.8
  20 ILE   (  22-)  A    -2.6
 135 THR   ( 143-)  A    -2.5
 257 PRO   ( 269-)  A    -2.5
 124 HIS   ( 132-)  A    -2.3
  56 HIS   (  64-)  A    -2.3
  16 HIS   (  18-)  A    -2.2
 187 PHE   ( 195-)  A    -2.1
  46 LEU   (  54-)  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.

  16 HIS   (  18-)  A  Poor phi/psi
  20 ILE   (  22-)  A  Poor phi/psi
  30 GLN   (  32-)  A  Poor phi/psi
  78 ASN   (  86-)  A  Poor phi/psi
 124 HIS   ( 132-)  A  Poor phi/psi
 152 GLY   ( 160-)  A  PRO omega poor
 164 ARG   ( 172-)  A  Poor phi/psi
 194 HIS   ( 202-)  A  Poor phi/psi
 204 VAL   ( 212-)  A  Poor phi/psi
 207 ASP   ( 215-)  A  Poor phi/psi
 209 LEU   ( 217-)  A  Poor phi/psi
 239 ASP   ( 251-)  A  Poor phi/psi
 256 PRO   ( 268-)  A  PRO omega poor
 279 HIS   ( 297-)  A  Poor phi/psi
 288 ASP   ( 306-)  A  Poor phi/psi
 297 PRO   ( 315-)  A  PRO omega poor
 315 ALA   ( 333-)  A  Poor phi/psi
 341 TYR   ( 359-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.485

Warning: Unusual backbone conformations

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

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

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

   3 PRO   (   5-)  A      0
  10 VAL   (  12-)  A      0
  11 PHE   (  13-)  A      0
  13 SER   (  15-)  A      0
  17 ALA   (  19-)  A      0
  18 TYR   (  20-)  A      0
  19 ARG   (  21-)  A      0
  20 ILE   (  22-)  A      0
  21 PRO   (  23-)  A      0
  30 GLN   (  32-)  A      0
  39 ARG   (  41-)  A      0
  40 ALA   (  42-)  A      0
  41 ALA   (  49-)  A      0
  42 GLU   (  50-)  A      0
  56 HIS   (  64-)  A      0
  61 GLN   (  69-)  A      0
  64 GLU   (  72-)  A      0
  67 ALA   (  75-)  A      0
  69 ALA   (  77-)  A      0
  70 ARG   (  78-)  A      0
  71 LEU   (  79-)  A      0
  72 ASP   (  80-)  A      0
  76 SER   (  84-)  A      0
  77 MET   (  85-)  A      0
  78 ASN   (  86-)  A      0
And so on for a total of 169 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 : 1.605

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].

 298 PRO   ( 316-)  A    41.6 envelop C-delta (36 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.

  86 GLN   (  94-)  A      NE2 <->  194 HIS   ( 202-)  A      NE2    0.24    2.76  INTRA BF
 106 GLN   ( 114-)  A      NE2 <->  361 HOH   (1082 )  A      O      0.22    2.48  INTRA
 200 ARG   ( 208-)  A      NH1 <->  361 HOH   (1116 )  A      O      0.18    2.52  INTRA
   1 SER   (   3-)  A      N   <->  307 VAL   ( 325-)  A    A CG1    0.16    2.94  INTRA BF
  80 CYS   (  88-)  A    A SG  <->  151 VAL   ( 159-)  A      C      0.16    3.24  INTRA BL
 179 ILE   ( 187-)  A      CG2 <->  180 GLN   ( 188-)  A      N      0.13    2.87  INTRA BF
 233 GLN   ( 245-)  A      NE2 <->  298 PRO   ( 316-)  A      O      0.13    2.57  INTRA
 320 GLN   ( 338-)  A      NE2 <->  361 HOH   (1144 )  A      O      0.12    2.58  INTRA
 174 ARG   ( 182-)  A      NH1 <->  361 HOH   (1094 )  A      O      0.12    2.58  INTRA
 229 ARG   ( 241-)  A      NH2 <->  361 HOH   (1192 )  A      O      0.11    2.59  INTRA BF
  84 ASP   (  92-)  A      O   <->   88 GLY   (  96-)  A      N      0.11    2.59  INTRA
  52 ASP   (  60-)  A      O   <->   56 HIS   (  64-)  A      N      0.11    2.59  INTRA
 132 ARG   ( 140-)  A      NE  <->  134 LEU   ( 142-)  A      CD2    0.10    3.00  INTRA
  29 GLN   (  31-)  A      NE2 <->  124 HIS   ( 132-)  A      ND1    0.10    2.90  INTRA
  80 CYS   (  88-)  A    A SG  <->  152 GLY   ( 160-)  A      CA     0.10    3.30  INTRA BL
   2 LEU   (   4-)  A      CB  <->    3 PRO   (   5-)  A      CD     0.09    3.01  INTRA BF
 155 HIS   ( 163-)  A      CD2 <->  318 ASP   ( 336-)  A      OD1    0.08    2.72  INTRA BL
 356 PRO   ( 374-)  A      O   <->  359 TYR   ( 377-)  A      N      0.07    2.63  INTRA BF
 177 HIS   ( 185-)  A      CD2 <->  179 ILE   ( 187-)  A      CG2    0.07    3.13  INTRA BF
   1 SER   (   3-)  A      N   <->  309 LEU   ( 327-)  A      CD2    0.06    3.04  INTRA BF
  48 ARG   (  56-)  A      NH2 <->  125 GLY   ( 133-)  A      C      0.05    3.05  INTRA
 356 PRO   ( 374-)  A      C   <->  358 GLU   ( 376-)  A      N      0.05    2.85  INTRA BF
 296 ARG   ( 314-)  A      N   <->  297 PRO   ( 315-)  A      CD     0.05    2.95  INTRA BL
  19 ARG   (  21-)  A      NE  <->  337 GLU   ( 355-)  A      OE2    0.05    2.65  INTRA BL
  32 LEU   (  34-)  A      N   <->   49 GLY   (  57-)  A      O      0.04    2.66  INTRA
 174 ARG   ( 182-)  A      NE  <->  361 HOH   (1095 )  A      O      0.04    2.66  INTRA
  84 ASP   (  92-)  A      OD2 <->  194 HIS   ( 202-)  A      ND1    0.04    2.66  INTRA
  53 ALA   (  61-)  A      N   <->   54 PRO   (  62-)  A      CD     0.03    2.97  INTRA
   5 LEU   (   7-)  A      O   <->   57 GLN   (  65-)  A      NE2    0.03    2.67  INTRA
 209 LEU   ( 217-)  A      CB  <->  210 GLU   ( 218-)  A      N      0.03    2.67  INTRA BL
 177 HIS   ( 185-)  A      ND1 <->  178 PRO   ( 186-)  A      CD     0.02    3.08  INTRA BF
 165 SER   ( 173-)  A      OG  <->  192 HIS   ( 200-)  A      ND1    0.02    2.68  INTRA BL
 271 ARG   ( 283-)  A      NH2 <->  358 GLU   ( 376-)  A      OE1    0.02    2.68  INTRA BF
 315 ALA   ( 333-)  A      CB  <->  316 TYR   ( 334-)  A      N      0.02    2.68  INTRA BL
 233 GLN   ( 245-)  A      O   <->  247 GLN   ( 259-)  A      N      0.01    2.69  INTRA BL
 219 VAL   ( 231-)  A      CG1 <->  220 VAL   ( 232-)  A      N      0.01    2.99  INTRA
  88 GLY   (  96-)  A      N   <->   89 THR   (  97-)  A      N      0.01    2.59  INTRA B3
 227 HIS   ( 239-)  A      N   <->  228 LEU   ( 240-)  A      N      0.01    2.59  INTRA BL
 279 HIS   ( 297-)  A      ND1 <->  280 PRO   ( 298-)  A      CD     0.01    3.09  INTRA BL
  37 GLU   (  39-)  A      OE2 <->   78 ASN   (  86-)  A      N      0.01    2.69  INTRA

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

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.

  39 ARG   (  41-)  A      -6.74
 258 GLN   ( 270-)  A      -6.25
 176 LEU   ( 184-)  A      -6.25
 296 ARG   ( 314-)  A      -6.24
 126 ARG   ( 134-)  A      -6.17
 181 ARG   ( 189-)  A      -6.12
 180 GLN   ( 188-)  A      -5.95
  86 GLN   (  94-)  A      -5.89
 311 LYS   ( 329-)  A      -5.50
  29 GLN   (  31-)  A      -5.44
 229 ARG   ( 241-)  A      -5.43
 196 ARG   ( 204-)  A      -5.17

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.

 179 ILE   ( 187-)  A       181 - ARG    189- ( A)         -5.40

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

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.

 302 ALA   ( 320-)  A   -2.79

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

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.

 361 HOH   (1072 )  A      O    -27.66   30.12   54.38
 361 HOH   (1092 )  A      O     -0.87   42.12   23.06
 361 HOH   (1170 )  A      O    -17.52   41.81   41.85
 361 HOH   (1212 )  A      O      0.09   43.31   28.22

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 361 HOH   (1189 )  A      O
 361 HOH   (1219 )  A      O
Marked this atom as acceptor  360  CL  (1001-) A     CL

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.

  56 HIS   (  64-)  A
  78 ASN   (  86-)  A
 124 HIS   ( 132-)  A
 244 GLN   ( 256-)  A
 258 GLN   ( 270-)  A
 285 GLN   ( 303-)  A
 320 GLN   ( 338-)  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.

   1 SER   (   3-)  A      N
   1 SER   (   3-)  A      OG
   2 LEU   (   4-)  A      N
  60 TRP   (  68-)  A      NE1
 100 GLN   ( 108-)  A      N
 102 THR   ( 110-)  A      OG1
 112 ASN   ( 120-)  A      ND2
 148 THR   ( 156-)  A      N
 151 VAL   ( 159-)  A      N
 171 TYR   ( 179-)  A      OH
 179 ILE   ( 187-)  A      N
 180 GLN   ( 188-)  A      N
 180 GLN   ( 188-)  A      NE2
 185 SER   ( 193-)  A      OG
 210 GLU   ( 218-)  A      N
 230 ALA   ( 242-)  A      N
 261 GLN   ( 273-)  A      N
 285 GLN   ( 303-)  A      NE2
 294 ASN   ( 312-)  A      ND2
 301 GLU   ( 319-)  A      N

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.

  42 GLU   (  50-)  A      OE2
  50 ASP   (  58-)  A      OD1
 118 GLN   ( 126-)  A      OE1

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.

 361 HOH   (1024 )  A      O  1.20  K  4 *2

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.

  42 GLU   (  50-)  A   H-bonding suggests Gln
 123 ASP   ( 131-)  A   H-bonding suggests Asn; but Alt-Rotamer
 254 GLU   ( 266-)  A   H-bonding suggests Gln; 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 :  -0.350
  2nd generation packing quality :  -1.237
  Ramachandran plot appearance   :  -1.651
  chi-1/chi-2 rotamer normality  :  -0.485
  Backbone conformation          :  -0.994

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.259 (tight)
  Bond angles                    :   0.657 (tight)
  Omega angle restraints         :   0.292 (tight)
  Side chain planarity           :   0.202 (tight)
  Improper dihedral distribution :   0.588
  B-factor distribution          :   0.465
  Inside/Outside distribution    :   0.984

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 : 1.76


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -1.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.259 (tight)
  Bond angles                    :   0.657 (tight)
  Omega angle restraints         :   0.292 (tight)
  Side chain planarity           :   0.202 (tight)
  Improper dihedral distribution :   0.588
  B-factor distribution          :   0.465
  Inside/Outside distribution    :   0.984
==============

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.