WHAT IF Check report

This file was created 2012-01-13 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 pdb1sa3.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.509
CA-only RMS fit for the two chains : 0.228

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Warning: 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: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
There is also strong SEQRES evidence for a multiplicity of: 2
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 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Administrative problems that can generate validation failures

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.

  68 LYS   (  32-)  A  -   CD
  68 LYS   (  32-)  A  -   CE
  68 LYS   (  32-)  A  -   NZ
 205 GLN   ( 169-)  A  -   CD
 205 GLN   ( 169-)  A  -   OE1
 205 GLN   ( 169-)  A  -   NE2
 290 LYS   ( 254-)  A  -   CG
 290 LYS   ( 254-)  A  -   CD
 290 LYS   ( 254-)  A  -   CE
 290 LYS   ( 254-)  A  -   NZ
 491 LYS   ( 193-)  B  -   CG
 491 LYS   ( 193-)  B  -   CD
 491 LYS   ( 193-)  B  -   CE
 491 LYS   ( 193-)  B  -   NZ
 552 LYS   ( 254-)  B  -   CG
 552 LYS   ( 254-)  B  -   CD
 552 LYS   ( 254-)  B  -   CE
 552 LYS   ( 254-)  B  -   NZ

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

  70 TYR   (  34-)  A
  87 TYR   (  51-)  A
 167 TYR   ( 131-)  A
 332 TYR   (  34-)  B
 349 TYR   (  51-)  B
 429 TYR   ( 131-)  B

Warning: Phenylalanine convention problem

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

  92 PHE   (  56-)  A
 140 PHE   ( 104-)  A
 142 PHE   ( 106-)  A
 218 PHE   ( 182-)  A
 243 PHE   ( 207-)  A
 296 PHE   ( 260-)  A
 402 PHE   ( 104-)  B
 404 PHE   ( 106-)  B
 480 PHE   ( 182-)  B
 505 PHE   ( 207-)  B

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.

  64 ASP   (  28-)  A
  80 ASP   (  44-)  A
 120 ASP   (  84-)  A
 326 ASP   (  28-)  B
 342 ASP   (  44-)  B
 382 ASP   (  84-)  B

Warning: Glutamic acid convention problem

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

  40 GLU   (   4-)  A
  95 GLU   (  59-)  A
 212 GLU   ( 176-)  A
 216 GLU   ( 180-)  A
 231 GLU   ( 195-)  A
 302 GLU   (   4-)  B
 357 GLU   (  59-)  B
 474 GLU   ( 176-)  B
 478 GLU   ( 180-)  B

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: 0.301
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.

   5 DCYT  (   5-)  C      C2'  C1'  N1  107.02   -4.5
   6 DGUA  (   6-)  C      C2'  C1'  N9  105.27   -5.6
   8 DGUA  (   8-)  C      N9   C8   N7  113.10    4.0
   9 DGUA  (   9-)  C      N9   C8   N7  113.11    4.0
  10 DCYT  (  12-)  D      O5'  C5'  C4' 118.24    5.7
  15 DGUA  (  17-)  D      N9   C8   N7  113.14    4.1
  23 DCYT  (   5-)  E      C2'  C1'  N1  106.15   -5.0
  24 DGUA  (   6-)  E      C2'  C1'  N9  104.84   -5.9
  25 DGUA  (   7-)  E      N9   C8   N7  113.14    4.1
  26 DGUA  (   8-)  E      N9   C8   N7  113.18    4.2
  32 DGUA  (  16-)  F      N9   C8   N7  113.12    4.0
  33 DGUA  (  17-)  F      N9   C8   N7  113.16    4.1

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: 0.634
RMS-deviation in bond angles: 1.238

Error: Nomenclature error(s)

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

  40 GLU   (   4-)  A
  64 ASP   (  28-)  A
  80 ASP   (  44-)  A
  95 GLU   (  59-)  A
 120 ASP   (  84-)  A
 212 GLU   ( 176-)  A
 216 GLU   ( 180-)  A
 231 GLU   ( 195-)  A
 302 GLU   (   4-)  B
 326 ASP   (  28-)  B
 342 ASP   (  44-)  B
 357 GLU   (  59-)  B
 382 ASP   (  84-)  B
 474 GLU   ( 176-)  B
 478 GLU   ( 180-)  B

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.

  71 GLU   (  35-)  A    4.55
 333 GLU   (  35-)  B    4.46

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.

 284 THR   ( 248-)  A    -3.0
 546 THR   ( 248-)  B    -2.9
 215 ARG   ( 179-)  A    -2.3
 457 SER   ( 159-)  B    -2.2
 195 SER   ( 159-)  A    -2.2
 477 ARG   ( 179-)  B    -2.2
 424 VAL   ( 126-)  B    -2.1
 162 VAL   ( 126-)  A    -2.1
 145 GLN   ( 109-)  A    -2.1
 378 VAL   (  80-)  B    -2.0
 376 ILE   (  78-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

 145 GLN   ( 109-)  A  Poor phi/psi
 165 ALA   ( 129-)  A  Poor phi/psi
 194 GLN   ( 158-)  A  Poor phi/psi
 195 SER   ( 159-)  A  Poor phi/psi
 224 THR   ( 188-)  A  Poor phi/psi
 225 LEU   ( 189-)  A  Poor phi/psi
 248 ARG   ( 212-)  A  Poor phi/psi
 277 PHE   ( 241-)  A  Poor phi/psi
 284 THR   ( 248-)  A  Poor phi/psi
 369 ASN   (  71-)  B  Poor phi/psi
 407 GLN   ( 109-)  B  Poor phi/psi
 427 ALA   ( 129-)  B  Poor phi/psi
 456 GLN   ( 158-)  B  Poor phi/psi
 457 SER   ( 159-)  B  Poor phi/psi
 487 LEU   ( 189-)  B  Poor phi/psi
 510 ARG   ( 212-)  B  Poor phi/psi
 536 LYS   ( 238-)  B  Poor phi/psi
 546 THR   ( 248-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.924

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.

 361 SER   (  63-)  B    0.34
 263 SER   ( 227-)  A    0.37
 305 SER   (   7-)  B    0.38
  63 SER   (  27-)  A    0.39

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 DCYT  (   3-)  C      0
   4 DCYT  (   4-)  C      0
   5 DCYT  (   5-)  C      0
   6 DGUA  (   6-)  C      0
   7 DGUA  (   7-)  C      0
   8 DGUA  (   8-)  C      0
   9 DGUA  (   9-)  C      0
  10 DCYT  (  12-)  D      0
  11 DCYT  (  13-)  D      0
  12 DCYT  (  14-)  D      0
  13 DCYT  (  15-)  D      0
  14 DGUA  (  16-)  D      0
  15 DGUA  (  17-)  D      0
  16 DGUA  (  18-)  D      0
  17 DGUA  (  19-)  D      0
  18 DGUA  (  20-)  D      0
  19 DCYT  (   1-)  E      0
  20 DCYT  (   2-)  E      0
  21 DCYT  (   3-)  E      0
  22 DCYT  (   4-)  E      0
  23 DCYT  (   5-)  E      0
  24 DGUA  (   6-)  E      0
  25 DGUA  (   7-)  E      0
  26 DGUA  (   8-)  E      0
  27 DGUA  (   9-)  E      0
And so on for a total of 216 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 : 1.270

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.

 404 PHE   ( 106-)  B      O   <->  407 GLN   ( 109-)  B      N      0.23    2.47  INTRA BF
   9 DGUA  (   9-)  C      OP1 <->  422 LYS   ( 124-)  B      NZ     0.21    2.49  INTRA BF
 334 LYS   (  36-)  B      NZ  <->  338 ASP   (  40-)  B      OD2    0.16    2.54  INTRA
 316 LEU   (  18-)  B      CD1 <->  327 ARG   (  29-)  B      NH1    0.16    2.94  INTRA BF
 344 GLU   (  46-)  B      CG  <->  345 SER   (  47-)  B      N      0.16    2.84  INTRA BF
  30 DCYT  (  14-)  F      C2' <->   31 DCYT  (  15-)  F      C5'    0.15    3.05  INTRA
   1 DCYT  (   1-)  C      N3  <->   18 DGUA  (  20-)  D      N1     0.14    2.86  INTRA BL
 410 ARG   ( 112-)  B      NH2 <->  493 GLU   ( 195-)  B      CG     0.13    2.97  INTRA BF
  12 DCYT  (  14-)  D      C2' <->   13 DCYT  (  15-)  D      C5'    0.13    3.07  INTRA
   5 DCYT  (   5-)  C      N3  <->   14 DGUA  (  16-)  D      N1     0.13    2.87  INTRA BL
 220 ARG   ( 184-)  A      NH1 <->  258 ILE   ( 222-)  A      CG2    0.13    2.97  INTRA
 192 ASN   ( 156-)  A      ND2 <->  569 HOH   ( 498 )  A      O      0.12    2.58  INTRA
  37 MET   (   1-)  A      N   <->  569 HOH   ( 544 )  A      O      0.12    2.58  INTRA
 468 ARG   ( 170-)  B      NH1 <->  471 GLU   ( 173-)  B      OE1    0.12    2.58  INTRA BF
  27 DGUA  (   9-)  E      OP1 <->  160 LYS   ( 124-)  A      NZ     0.12    2.58  INTRA BF
  24 DGUA  (   6-)  E      OP1 <->  418 HIS   ( 120-)  B      ND1    0.10    2.60  INTRA BL
 350 ASN   (  52-)  B      ND2 <->  372 LEU   (  74-)  B      CD2    0.10    3.00  INTRA BF
 211 LEU   ( 175-)  A      O   <->  214 TYR   ( 178-)  A      N      0.10    2.60  INTRA BL
   6 DGUA  (   6-)  C      N1  <->   13 DCYT  (  15-)  D      N3     0.09    2.91  INTRA BL
 533 LYS   ( 235-)  B      O   <->  536 LYS   ( 238-)  B      N      0.09    2.61  INTRA BF
  23 DCYT  (   5-)  E      N3  <->   32 DGUA  (  16-)  F      N1     0.08    2.92  INTRA BL
  19 DCYT  (   1-)  E      N3  <->   36 DGUA  (  20-)  F      N1     0.08    2.92  INTRA
  24 DGUA  (   6-)  E      N1  <->   31 DCYT  (  15-)  F      N3     0.08    2.92  INTRA BL
 536 LYS   ( 238-)  B      N   <->  537 PRO   ( 239-)  B      CD     0.08    2.92  INTRA
 460 LEU   ( 162-)  B      N   <->  570 HOH   ( 434 )  B      O      0.08    2.62  INTRA
And so on for a total of 72 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 535 ARG   ( 237-)  B      -7.27
 273 ARG   ( 237-)  A      -7.07
 387 ARG   (  89-)  B      -5.83
 315 GLN   (  17-)  B      -5.73
  53 GLN   (  17-)  A      -5.72
 423 LYS   ( 125-)  B      -5.28
 125 ARG   (  89-)  A      -5.22
 161 LYS   ( 125-)  A      -5.14
 229 LYS   ( 193-)  A      -5.10
 491 LYS   ( 193-)  B      -5.00

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.

 276 GLY   ( 240-)  A       278 - GLY    242- ( A)         -4.20
 538 GLY   ( 240-)  B       540 - GLY    242- ( B)         -4.19

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 535 ARG   ( 237-)  B   -3.39
 144 ASN   ( 108-)  A   -3.22
 288 GLY   ( 252-)  A   -3.03
 550 GLY   ( 252-)  B   -3.01
 162 VAL   ( 126-)  A   -2.97
 424 VAL   ( 126-)  B   -2.95
 291 ALA   ( 255-)  A   -2.52
 387 ARG   (  89-)  B   -2.50

Warning: Abnormal packing Z-score for sequential residues

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

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

 194 GLN   ( 158-)  A     -  197 LYS   ( 161-)  A        -1.81
 456 GLN   ( 158-)  B     -  459 LYS   ( 161-)  B        -1.81

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 565 HOH   (  34 )  C      O     -5.07   62.08   47.45

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   (  20-)  A
  90 ASN   (  54-)  A
 143 HIS   ( 107-)  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.

  80 ASP   (  44-)  A      N
  89 THR   (  53-)  A      N
 134 THR   (  98-)  A      N
 314 ASP   (  16-)  B      N
 319 THR   (  21-)  B      N
 323 VAL   (  25-)  B      N
 342 ASP   (  44-)  B      N
 343 ILE   (  45-)  B      N
 351 THR   (  53-)  B      N
 373 ASP   (  75-)  B      N
 396 THR   (  98-)  B      N
 446 LYS   ( 148-)  B      N
 519 ASN   ( 221-)  B      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.

 320 GLN   (  22-)  B      OE1
 374 ASN   (  76-)  B      OD1

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.

 569 HOH   ( 432 )  A      O  0.89  K  5
 569 HOH   ( 433 )  A      O  0.87  K  4
 569 HOH   ( 502 )  A      O  0.95  K  4
 570 HOH   ( 409 )  B      O  1.03  K  4 NCS 1/1

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.

 135 ASP   (  99-)  A   H-bonding suggests Asn
 500 ASP   ( 202-)  B   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 :   0.136
  2nd generation packing quality :  -1.183
  Ramachandran plot appearance   :  -0.445
  chi-1/chi-2 rotamer normality  :  -0.924
  Backbone conformation          :  -0.321

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.301 (tight)
  Bond angles                    :   0.634 (tight)
  Omega angle restraints         :   0.231 (tight)
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.575
  B-factor distribution          :   0.753
  Inside/Outside distribution    :   0.956

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 : 1.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.301 (tight)
  Bond angles                    :   0.634 (tight)
  Omega angle restraints         :   0.231 (tight)
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.575
  B-factor distribution          :   0.753
  Inside/Outside distribution    :   0.956
==============

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.