WHAT IF Check report

This file was created 2012-01-29 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 pdb3a45.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 : 0.956
CA-only RMS fit for the two chains : 0.597

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: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

 579   K   ( 290-)  B  A

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.

  83 LEU   (  84-)  A  -   CD1
  83 LEU   (  84-)  A  -   CD2
 148 LYS   ( 149-)  A  -   CG
 148 LYS   ( 149-)  A  -   CD
 148 LYS   ( 149-)  A  -   CE
 148 LYS   ( 149-)  A  -   NZ
 536 ASP   ( 249-)  B  -   CB
 536 ASP   ( 249-)  B  -   CG
 536 ASP   ( 249-)  B  -   OD1
 536 ASP   ( 249-)  B  -   OD2
 574 LYS   ( 287-)  B  -   CB
 574 LYS   ( 287-)  B  -   CG
 574 LYS   ( 287-)  B  -   CD
 574 LYS   ( 287-)  B  -   CE
 574 LYS   ( 287-)  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: Artificial side chains detected

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

 418 LYS   ( 131-)  B
 551 VAL   ( 264-)  B

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.

 433 ASP   ( 146-)  B    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

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.79

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: Arginine nomenclature problem

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

 401 ARG   ( 114-)  B

Warning: Tyrosine convention problem

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

  94 TYR   (  95-)  A
 173 TYR   ( 174-)  A
 207 TYR   ( 208-)  A
 252 TYR   ( 253-)  A
 382 TYR   (  95-)  B
 461 TYR   ( 174-)  B
 495 TYR   ( 208-)  B
 540 TYR   ( 253-)  B

Warning: Phenylalanine convention problem

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

  43 PHE   (  44-)  A
 118 PHE   ( 119-)  A
 138 PHE   ( 139-)  A
 247 PHE   ( 248-)  A
 315 PHE   (  28-)  B
 331 PHE   (  44-)  B
 406 PHE   ( 119-)  B
 426 PHE   ( 139-)  B
 535 PHE   ( 248-)  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.

  26 ASP   (  27-)  A
  41 ASP   (  42-)  A
  42 ASP   (  43-)  A
  67 ASP   (  68-)  A
 102 ASP   ( 103-)  A
 143 ASP   ( 144-)  A
 185 ASP   ( 186-)  A
 248 ASP   ( 249-)  A
 266 ASP   ( 267-)  A
 329 ASP   (  42-)  B
 358 ASP   (  71-)  B
 390 ASP   ( 103-)  B
 536 ASP   ( 249-)  B
 545 ASP   ( 258-)  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.

  14 GLU   (  15-)  A
  36 GLU   (  37-)  A
  38 GLU   (  39-)  A
  64 GLU   (  65-)  A
 124 GLU   ( 125-)  A
 133 GLU   ( 134-)  A
 199 GLU   ( 200-)  A
 302 GLU   (  15-)  B
 324 GLU   (  37-)  B
 352 GLU   (  65-)  B
 379 GLU   (  92-)  B
 485 GLU   ( 198-)  B
 515 GLU   ( 228-)  B
 534 GLU   ( 247-)  B

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998322 -0.000029  0.000110|
 | -0.000029  0.998977  0.000041|
 |  0.000110  0.000041  0.999069|
Proposed new scale matrix

 |  0.025901  0.001547  0.005225|
 |  0.000000  0.018428  0.005958|
 | -0.000001  0.000000  0.012229|
With corresponding cell

    A    =  38.608  B   =  54.363  C    =  87.221
    Alpha= 107.000  Beta=  99.840  Gamma=  93.421

The CRYST1 cell dimensions

    A    =  38.673  B   =  54.417  C    =  87.308
    Alpha= 107.000  Beta=  99.860  Gamma=  93.420

Variance: 29.178
(Under-)estimated Z-score: 3.981

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.

 342 VAL   (  55-)  B      N    CA   C    99.96   -4.0
 562 ASN   ( 275-)  B      N    CA   C    99.70   -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.

  14 GLU   (  15-)  A
  26 ASP   (  27-)  A
  36 GLU   (  37-)  A
  38 GLU   (  39-)  A
  41 ASP   (  42-)  A
  42 ASP   (  43-)  A
  64 GLU   (  65-)  A
  67 ASP   (  68-)  A
 102 ASP   ( 103-)  A
 124 GLU   ( 125-)  A
 133 GLU   ( 134-)  A
 143 ASP   ( 144-)  A
 185 ASP   ( 186-)  A
 199 GLU   ( 200-)  A
 248 ASP   ( 249-)  A
 266 ASP   ( 267-)  A
 302 GLU   (  15-)  B
 324 GLU   (  37-)  B
 329 ASP   (  42-)  B
 352 GLU   (  65-)  B
 358 ASP   (  71-)  B
 379 GLU   (  92-)  B
 390 ASP   ( 103-)  B
 401 ARG   ( 114-)  B
 485 GLU   ( 198-)  B
 515 GLU   ( 228-)  B
 534 GLU   ( 247-)  B
 536 ASP   ( 249-)  B
 545 ASP   ( 258-)  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.

  17 PHE   (  18-)  A    4.47
  27 PHE   (  28-)  A    4.03

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.

 382 TYR   (  95-)  B    -2.3
 572 ILE   ( 285-)  B    -2.2
   3 GLY   (   4-)  A    -2.2
 421 GLU   ( 134-)  B    -2.2
 341 ASN   (  54-)  B    -2.1
 269 ILE   ( 270-)  A    -2.1
 431 ASP   ( 144-)  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.

   3 GLY   (   4-)  A  Poor phi/psi
  47 LEU   (  48-)  A  PRO omega poor
  94 TYR   (  95-)  A  Poor phi/psi
 103 ASN   ( 104-)  A  Poor phi/psi
 104 GLU   ( 105-)  A  Poor phi/psi
 114 ASN   ( 115-)  A  Poor phi/psi
 251 VAL   ( 252-)  A  Poor phi/psi
 253 ARG   ( 254-)  A  Poor phi/psi
 260 GLY   ( 261-)  A  Poor phi/psi
 291 GLY   (   4-)  B  Poor phi/psi
 335 LEU   (  48-)  B  PRO omega poor
 357 ASN   (  70-)  B  Poor phi/psi
 382 TYR   (  95-)  B  Poor phi/psi
 391 ASN   ( 104-)  B  Poor phi/psi
 392 GLU   ( 105-)  B  Poor phi/psi
 402 ASN   ( 115-)  B  Poor phi/psi
 441 LYS   ( 154-)  B  Poor phi/psi
 471 LYS   ( 184-)  B  Poor phi/psi
 541 ARG   ( 254-)  B  Poor phi/psi
 560 GLY   ( 273-)  B  Poor phi/psi
 562 ASN   ( 275-)  B  Poor phi/psi
 575 LEU   ( 288-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.723

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!

  18 LYS   (  19-)  A      0
  23 GLU   (  24-)  A      0
  24 TYR   (  25-)  A      0
  29 SER   (  30-)  A      0
  31 ARG   (  32-)  A      0
  34 LYS   (  35-)  A      0
  35 SER   (  36-)  A      0
  38 GLU   (  39-)  A      0
  46 ASN   (  47-)  A      0
  47 LEU   (  48-)  A      0
  53 ASN   (  54-)  A      0
  57 LYS   (  58-)  A      0
  59 LYS   (  60-)  A      0
  69 ASN   (  70-)  A      0
  75 TRP   (  76-)  A      0
  83 LEU   (  84-)  A      0
  84 THR   (  85-)  A      0
  87 TRP   (  88-)  A      0
  93 LYS   (  94-)  A      0
  94 TYR   (  95-)  A      0
  95 THR   (  96-)  A      0
 104 GLU   ( 105-)  A      0
 105 LEU   ( 106-)  A      0
 113 ARG   ( 114-)  A      0
 114 ASN   ( 115-)  A      0
And so on for a total of 240 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 : 1.317

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.

  53 ASN   (  54-)  A      ND2 <->  581 HOH   (1339 )  A      O      0.29    2.41  INTRA BL
 562 ASN   ( 275-)  B      N   <->  563 LYS   ( 276-)  B      N      0.26    2.34  INTRA BF
 347 LYS   (  60-)  B      NZ  <->  582 HOH   (1287 )  B      O      0.23    2.47  INTRA BL
 392 GLU   ( 105-)  B      N   <->  582 HOH   (1143 )  B      O      0.23    2.47  INTRA
 164 LYS   ( 165-)  A      NZ  <->  581 HOH   (1161 )  A      O      0.23    2.47  INTRA
 559 SER   ( 272-)  B      O   <->  561 LYS   ( 274-)  B      N      0.22    2.48  INTRA BF
 232 GLY   ( 233-)  A      N   <->  581 HOH   (1282 )  A      O      0.21    2.49  INTRA
 347 LYS   (  60-)  B      NZ  <->  582 HOH   (1219 )  B      O      0.20    2.50  INTRA
  34 LYS   (  35-)  A      N   <->  581 HOH   (1123 )  A      O      0.19    2.51  INTRA BL
 187 HIS   ( 188-)  A      NE2 <->  581 HOH   (1296 )  A      O      0.18    2.52  INTRA
  19 GLY   (  20-)  A      N   <->   51 VAL   (  52-)  A      O      0.18    2.52  INTRA BL
 545 ASP   ( 258-)  B      OD1 <->  548 GLY   ( 261-)  B      N      0.17    2.53  INTRA BF
  20 LYS   (  21-)  A      NZ  <->  581 HOH   (1135 )  A      O      0.17    2.53  INTRA BL
 290 GLU   (   3-)  B      CD  <->  459 GLY   ( 172-)  B      CA     0.17    3.03  INTRA BL
 450 ASP   ( 163-)  B      CG  <->  453 LYS   ( 166-)  B      CG     0.15    3.05  INTRA
  74 LYS   (  75-)  A      NZ  <->  581 HOH   (1452 )  A      O      0.15    2.55  INTRA
 194 THR   ( 195-)  A      N   <->  197 GLU   ( 198-)  A      OE1    0.15    2.55  INTRA BF
 550 LYS   ( 263-)  B      NZ  <->  552 ILE   ( 265-)  B      CG2    0.14    2.96  INTRA BF
 555 LYS   ( 268-)  B      NZ  <->  582 HOH   (1396 )  B      O      0.14    2.56  INTRA BF
 254 LYS   ( 255-)  A      NZ  <->  581 HOH   (1427 )  A      O      0.14    2.56  INTRA
 257 ASP   ( 258-)  A      OD1 <->  261 ASN   ( 262-)  A      N      0.14    2.56  INTRA BF
 319 ARG   (  32-)  B      NH2 <->  582 HOH   (1120 )  B      O      0.14    2.56  INTRA BL
  71 LYS   (  72-)  A      N   <->  326 GLU   (  39-)  B      OE1    0.13    2.57  INTRA BL
 494 LYS   ( 207-)  B      NZ  <->  582 HOH   (1059 )  B      O      0.13    2.57  INTRA
 417 ARG   ( 130-)  B      NH1 <->  582 HOH   (1191 )  B      O      0.13    2.57  INTRA
And so on for a total of 101 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.

 220 TYR   ( 221-)  A      -6.71
 508 TYR   ( 221-)  B      -6.50
  83 LEU   (  84-)  A      -6.36
 245 LYS   ( 246-)  A      -6.03
 533 LYS   ( 246-)  B      -6.00
 253 ARG   ( 254-)  A      -5.88
 217 HIS   ( 218-)  A      -5.40
 561 LYS   ( 274-)  B      -5.36
 287 LEU   ( 288-)  A      -5.30
 529 HIS   ( 242-)  B      -5.23
 192 ASN   ( 193-)  A      -5.18
 334 ASN   (  47-)  B      -5.16
  46 ASN   (  47-)  A      -5.16
 480 ASN   ( 193-)  B      -5.15
 274 ASN   ( 275-)  A      -5.13
 241 HIS   ( 242-)  A      -5.11
 505 HIS   ( 218-)  B      -5.09
 371 LEU   (  84-)  B      -5.07

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.

 381 LYS   (  94-)  B   -2.71
 284 ILE   ( 285-)  A   -2.61
 510 VAL   ( 223-)  B   -2.60
 536 ASP   ( 249-)  B   -2.54

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.

  91 GLU   (  92-)  A     -   94 TYR   (  95-)  A        -1.43
 509 MET   ( 222-)  B     -  513 GLU   ( 226-)  B        -1.96

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.

 581 HOH   (1280 )  A      O    -16.67  -10.32    6.76
 581 HOH   (1515 )  A      O    -22.59  -18.57   14.80
 582 HOH   (1327 )  B      O      8.99    8.50   15.75
 582 HOH   (1381 )  B      O      6.02  -27.56   14.32

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.

  53 ASN   (  54-)  A
  73 ASN   (  74-)  A
 103 ASN   ( 104-)  A
 132 ASN   ( 133-)  A
 223 ASN   ( 224-)  A
 241 HIS   ( 242-)  A
 334 ASN   (  47-)  B
 361 ASN   (  74-)  B
 410 ASN   ( 123-)  B
 511 ASN   ( 224-)  B
 573 GLN   ( 286-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  25 ILE   (  26-)  A      N
  29 SER   (  30-)  A      N
  79 ASN   (  80-)  A      ND2
  90 PHE   (  91-)  A      N
 144 ILE   ( 145-)  A      N
 148 LYS   ( 149-)  A      N
 154 GLN   ( 155-)  A      N
 223 ASN   ( 224-)  A      N
 253 ARG   ( 254-)  A      N
 259 ASN   ( 260-)  A      N
 313 ILE   (  26-)  B      N
 320 TYR   (  33-)  B      N
 326 GLU   (  39-)  B      N
 367 ASN   (  80-)  B      ND2
 378 PHE   (  91-)  B      N
 413 LYS   ( 126-)  B      N
 431 ASP   ( 144-)  B      N
 432 ILE   ( 145-)  B      N
 473 ASP   ( 186-)  B      N
 475 HIS   ( 188-)  B      N
 504 ASN   ( 217-)  B      N
 511 ASN   ( 224-)  B      N
 514 ASN   ( 227-)  B      N
 524 TYR   ( 237-)  B      N
 534 GLU   ( 247-)  B      N
 541 ARG   ( 254-)  B      N
 543 LYS   ( 256-)  B      N
 557 ILE   ( 270-)  B      N
 563 LYS   ( 276-)  B      N
 568 TRP   ( 281-)  B      NE1
 575 LEU   ( 288-)  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.

 208 GLU   ( 209-)  A      OE2
 496 GLU   ( 209-)  B      OE2

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+.

 579   K   ( 290-)  B    0.65  -.-   Poor packing (Few ligands (4) )
 580   K   ( 290-)  B   -.-  -.-  Too few ligands (2)

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.

 581 HOH   (1050 )  A      O  1.14  K  4 *1
 581 HOH   (1193 )  A      O  0.97  K  6 *1 Ion-B
 581 HOH   (1301 )  A      O  1.10  K  4 *1
 581 HOH   (1524 )  A      O  1.10  K  4 *1 Ion-B
 582 HOH   (1134 )  B      O  0.92  K  4 *1
 582 HOH   (1458 )  B      O  0.94  K  5 *1 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.

  11 ASP   (  12-)  A   H-bonding suggests Asn; but Alt-Rotamer
  36 GLU   (  37-)  A   H-bonding suggests Gln; but Alt-Rotamer
 143 ASP   ( 144-)  A   H-bonding suggests Asn; but Alt-Rotamer
 214 ASP   ( 215-)  A   H-bonding suggests Asn; but Alt-Rotamer
 248 ASP   ( 249-)  A   H-bonding suggests Asn; but Alt-Rotamer
 257 ASP   ( 258-)  A   H-bonding suggests Asn; but Alt-Rotamer
 299 ASP   (  12-)  B   H-bonding suggests Asn; but Alt-Rotamer
 421 GLU   ( 134-)  B   H-bonding suggests Gln; but Alt-Rotamer
 502 ASP   ( 215-)  B   H-bonding suggests Asn; but Alt-Rotamer
 536 ASP   ( 249-)  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 :  -0.358
  2nd generation packing quality :  -2.260
  Ramachandran plot appearance   :  -1.520
  chi-1/chi-2 rotamer normality  :  -1.723
  Backbone conformation          :  -0.702

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.263 (tight)
  Bond angles                    :   0.569 (tight)
  Omega angle restraints         :   0.240 (tight)
  Side chain planarity           :   0.227 (tight)
  Improper dihedral distribution :   0.564
  B-factor distribution          :   0.790
  Inside/Outside distribution    :   0.996

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.263 (tight)
  Bond angles                    :   0.569 (tight)
  Omega angle restraints         :   0.240 (tight)
  Side chain planarity           :   0.227 (tight)
  Improper dihedral distribution :   0.564
  B-factor distribution          :   0.790
  Inside/Outside distribution    :   0.996
==============

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.