WHAT IF Check report

This file was created 2011-12-17 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 pdb1pyw.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 70460.867
Volume of the Unit Cell V= 3135011.8
Space group multiplicity: 9
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.944
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.840

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 611 ACE   (   0-)  C  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 370 PHE   (   1-)  C  -   N   bound to  611 ACE   (   0-)  C  -   C

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.

 288 LEU   ( 109-)  B  -   CB
 288 LEU   ( 109-)  B  -   CG
 288 LEU   ( 109-)  B  -   CD1
 288 LEU   ( 109-)  B  -   CD2
 289 GLN   ( 110-)  B  -   CB
 289 GLN   ( 110-)  B  -   CG
 289 GLN   ( 110-)  B  -   CD
 289 GLN   ( 110-)  B  -   OE1
 289 GLN   ( 110-)  B  -   NE2
 290 HIS   ( 111-)  B  -   CB
 290 HIS   ( 111-)  B  -   CG
 290 HIS   ( 111-)  B  -   ND1
 290 HIS   ( 111-)  B  -   CD2
 290 HIS   ( 111-)  B  -   CE1
 290 HIS   ( 111-)  B  -   NE2
 291 HIS   ( 112-)  B  -   CB
 291 HIS   ( 112-)  B  -   CG
 291 HIS   ( 112-)  B  -   ND1
 291 HIS   ( 112-)  B  -   CD2
 291 HIS   ( 112-)  B  -   CE1
 291 HIS   ( 112-)  B  -   NE2
 434 LYS   (  56-)  D  -   CB
 434 LYS   (  56-)  D  -   CG
 434 LYS   (  56-)  D  -   CD
 434 LYS   (  56-)  D  -   CE
 434 LYS   (  56-)  D  -   NZ
 435 LYS   (  57-)  D  -   CB
 435 LYS   (  57-)  D  -   CG
 435 LYS   (  57-)  D  -   CD
 435 LYS   (  57-)  D  -   CE
 435 LYS   (  57-)  D  -   NZ

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone 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. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 288 LEU   ( 109-)  B  -   N
 288 LEU   ( 109-)  B  -   CA
 288 LEU   ( 109-)  B  -   C
 288 LEU   ( 109-)  B  -   O
 289 GLN   ( 110-)  B  -   N
 289 GLN   ( 110-)  B  -   CA
 289 GLN   ( 110-)  B  -   C
 289 GLN   ( 110-)  B  -   O
 290 HIS   ( 111-)  B  -   N
 290 HIS   ( 111-)  B  -   CA
 290 HIS   ( 111-)  B  -   C
 290 HIS   ( 111-)  B  -   O
 291 HIS   ( 112-)  B  -   N
 291 HIS   ( 112-)  B  -   CA
 291 HIS   ( 112-)  B  -   C
 291 HIS   ( 112-)  B  -   O
 434 LYS   (  56-)  D  -   N
 434 LYS   (  56-)  D  -   CA
 434 LYS   (  56-)  D  -   C
 434 LYS   (  56-)  D  -   O
 435 LYS   (  57-)  D  -   N
 435 LYS   (  57-)  D  -   CA
 435 LYS   (  57-)  D  -   C
 435 LYS   (  57-)  D  -   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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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.

 376 MAA   (   7-)  C
 433 ASP   (  55-)  D

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

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

  47 ARG   (  50-)  A
 250 ARG   (  71-)  B
 259 ARG   (  80-)  B
 309 ARG   ( 130-)  B

Warning: Tyrosine convention problem

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

 147 TYR   ( 150-)  A
 226 TYR   (  47-)  B
 281 TYR   ( 102-)  B
 406 TYR   (  28-)  D
 455 TYR   (  77-)  D
 463 TYR   (  85-)  D
 543 TYR   ( 174-)  D
 550 TYR   ( 181-)  D
 554 TYR   ( 185-)  D
 567 TYR   ( 198-)  D
 586 TYR   ( 217-)  D

Warning: Phenylalanine convention problem

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

 109 PHE   ( 112-)  A
 192 PHE   (  13-)  B
 422 PHE   (  44-)  D
 423 PHE   (  45-)  D
 492 PHE   ( 123-)  D
 565 PHE   ( 196-)  D

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.

 168 ASP   ( 171-)  A
 383 ASP   (   5-)  D
 388 ASP   (  10-)  D
 407 ASP   (  29-)  D
 420 ASP   (  42-)  D
 433 ASP   (  55-)  D
 440 ASP   (  62-)  D
 529 ASP   ( 160-)  D

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.

   1 GLU   (   4-)  A
  27 GLU   (  30-)  A
  44 GLU   (  47-)  A
  52 GLU   (  55-)  A
  68 GLU   (  71-)  A
  95 GLU   (  98-)  A
 155 GLU   ( 158-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 201 GLU   (  22-)  B
 238 GLU   (  59-)  B
 248 GLU   (  69-)  B
 341 GLU   ( 162-)  B
 355 GLU   ( 176-)  B
 445 GLU   (  67-)  D
 488 GLU   ( 119-)  D
 527 GLU   ( 158-)  D

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

 |  0.998603 -0.000403  0.000204|
 | -0.000403  0.998838  0.000314|
 |  0.000204  0.000314  0.998776|
Proposed new scale matrix

 |  0.005806  0.003353 -0.000002|
 |  0.000003  0.006702 -0.000002|
 | -0.000002 -0.000003  0.008230|
With corresponding cell

    A    = 172.262  B   = 172.349  C    = 121.506
    Alpha=  89.980  Beta=  89.977  Gamma= 120.030

The CRYST1 cell dimensions

    A    = 172.507  B   = 172.507  C    = 121.652
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 34.836
(Under-)estimated Z-score: 4.350

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.

  85 GLU   (  88-)  A      N    CA   C    97.68   -4.8
 343 VAL   ( 164-)  B      N    CA   C    98.30   -4.6
 459 VAL   (  81-)  D      N    CA   C    99.93   -4.0

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.

   1 GLU   (   4-)  A
  27 GLU   (  30-)  A
  44 GLU   (  47-)  A
  47 ARG   (  50-)  A
  52 GLU   (  55-)  A
  68 GLU   (  71-)  A
  95 GLU   (  98-)  A
 155 GLU   ( 158-)  A
 168 ASP   ( 171-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 201 GLU   (  22-)  B
 238 GLU   (  59-)  B
 248 GLU   (  69-)  B
 250 ARG   (  71-)  B
 259 ARG   (  80-)  B
 309 ARG   ( 130-)  B
 341 GLU   ( 162-)  B
 355 GLU   ( 176-)  B
 383 ASP   (   5-)  D
 388 ASP   (  10-)  D
 407 ASP   (  29-)  D
 420 ASP   (  42-)  D
 433 ASP   (  55-)  D
 440 ASP   (  62-)  D
 445 GLU   (  67-)  D
 488 GLU   ( 119-)  D
 527 GLU   ( 158-)  D
 529 ASP   ( 160-)  D

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.

  85 GLU   (  88-)  A    5.07
 343 VAL   ( 164-)  B    4.53
 402 MET   (  24-)  D    4.22
 373 GLN   (   4-)  C    4.17

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.

 110 THR   ( 113-)  A    -2.6
  13 PRO   (  16-)  A    -2.5
 150 PHE   ( 153-)  A    -2.4
 547 SER   ( 178-)  D    -2.4
 336 THR   ( 157-)  B    -2.3
 217 VAL   (  38-)  B    -2.2
 202 ARG   (  23-)  B    -2.1
 208 ARG   (  29-)  B    -2.1
 514 PHE   ( 145-)  D    -2.1
 415 LYS   (  37-)  D    -2.1
 333 THR   ( 154-)  B    -2.0
 478 THR   ( 109-)  D    -2.0
 495 GLY   ( 126-)  D    -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.

  12 ASN   (  15-)  A  PRO omega poor
  15 GLN   (  18-)  A  Poor phi/psi
  36 LYS   (  39-)  A  Poor phi/psi
  75 ASN   (  78-)  A  Poor phi/psi
  97 ARG   ( 100-)  A  Poor phi/psi
 110 THR   ( 113-)  A  PRO omega poor
 121 ASN   ( 124-)  A  Poor phi/psi
 126 THR   ( 129-)  A  Poor phi/psi
 140 HIS   ( 143-)  A  Poor phi/psi
 198 ASN   (  19-)  B  Poor phi/psi
 211 TYR   (  32-)  B  Poor phi/psi
 285 THR   ( 106-)  B  Poor phi/psi
 286 GLN   ( 107-)  B  Poor phi/psi
 287 PRO   ( 108-)  B  Poor phi/psi
 289 GLN   ( 110-)  B  Poor phi/psi
 290 HIS   ( 111-)  B  Poor phi/psi
 302 TYR   ( 123-)  B  PRO omega poor
 313 ASN   ( 134-)  B  Poor phi/psi
 332 TRP   ( 153-)  B  Poor phi/psi
 410 TYR   (  32-)  D  Poor phi/psi
 415 LYS   (  37-)  D  Poor phi/psi
 435 LYS   (  57-)  D  Poor phi/psi
 470 ASN   (  92-)  D  Poor phi/psi
 473 PHE   (  95-)  D  Poor phi/psi
 494 ASN   ( 125-)  D  Poor phi/psi
 495 GLY   ( 126-)  D  Poor phi/psi
 507 ASN   ( 138-)  D  Poor phi/psi
 508 LYS   ( 139-)  D  Poor phi/psi
 547 SER   ( 178-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.354

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.

 580 SER   ( 211-)  D    0.37

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!

   8 GLU   (  11-)  A      0
  12 ASN   (  15-)  A      0
  15 GLN   (  18-)  A      0
  16 SER   (  19-)  A      0
  19 PHE   (  22-)  A      0
  23 PHE   (  26-)  A      0
  29 PHE   (  32-)  A      0
  30 HIS   (  33-)  A      0
  36 LYS   (  39-)  A      0
  41 ARG   (  44-)  A      0
  48 PHE   (  51-)  A      0
  50 SER   (  53-)  A      0
  76 TYR   (  79-)  A      0
  96 LEU   (  99-)  A      0
  97 ARG   ( 100-)  A      0
 100 ASN   ( 103-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 109 PHE   ( 112-)  A      0
 110 THR   ( 113-)  A      0
 112 PRO   ( 115-)  A      0
 113 VAL   ( 116-)  A      0
 120 ARG   ( 123-)  A      0
 121 ASN   ( 124-)  A      0
 125 VAL   ( 128-)  A      0
And so on for a total of 262 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 : 1.469

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 304 GLY   ( 125-)  B   1.59   37

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.

 289 GLN   ( 110-)  B      O   <->  291 HIS   ( 112-)  B      N      0.34    2.36  INTRA BL
 329 ASN   ( 150-)  B      ND2 <->  333 THR   ( 154-)  B      CG2    0.26    2.84  INTRA
 587 ASN   ( 218-)  D      ND2 <->  616 HOH   ( 258 )  D      O      0.25    2.45  INTRA
  73 ARG   (  76-)  A      NH2 <->  236 ASP   (  57-)  B      OD2    0.24    2.46  INTRA BL
 231 GLU   (  52-)  B      OE2 <->  234 ARG   (  55-)  B      NE     0.24    2.46  INTRA BF
 181 ASP   (   2-)  B      OD1 <->  185 ARG   (   6-)  B      NH2    0.21    2.49  INTRA BL
 181 ASP   (   2-)  B      CG  <->  185 ARG   (   6-)  B      NH2    0.18    2.92  INTRA
 471 CYS   (  93-)  D      SG  <->  479 CYS   ( 110-)  D      N      0.18    3.12  INTRA BL
 386 PRO   (   8-)  D      O   <->  391 LYS   (  13-)  D      NZ     0.18    2.52  INTRA BF
 143 ARG   ( 146-)  A      NH1 <->  613 HOH   ( 198 )  A      O      0.18    2.52  INTRA
 494 ASN   ( 125-)  D      O   <->  496 ASN   ( 127-)  D      N      0.17    2.53  INTRA BF
 204 ARG   (  25-)  B      NH2 <->  220 ASP   (  41-)  B      OD2    0.17    2.53  INTRA
 181 ASP   (   2-)  B      OD1 <->  183 ARG   (   4-)  B      CD     0.16    2.64  INTRA BL
 239 TYR   (  60-)  B      CE2 <->  243 GLN   (  64-)  B      NE2    0.15    2.95  INTRA
 471 CYS   (  93-)  D      SG  <->  478 THR   ( 109-)  D      C      0.14    3.26  INTRA BL
 446 LEU   (  68-)  D      C   <->  587 ASN   ( 218-)  D      ND2    0.14    2.96  INTRA
 187 LEU   (   8-)  B      O   <->  211 TYR   (  32-)  B      O      0.13    2.12  INTRA
 115 ASN   ( 118-)  A      ND2 <->  163 GLU   ( 166-)  A      OE1    0.13    2.57  INTRA BF
 140 HIS   ( 143-)  A      CD2 <->  191 LYS   (  12-)  B      NZ     0.13    2.97  INTRA BL
 400 GLY   (  22-)  D      N   <->  545 PHE   ( 176-)  D      O      0.12    2.58  INTRA
  91 ASN   (  94-)  A      ND2 <->  101 VAL   ( 104-)  A      CB     0.12    2.98  INTRA BF
  43 GLU   (  46-)  A      OE2 <->   47 ARG   (  50-)  A      NE     0.11    2.59  INTRA BF
 125 VAL   ( 128-)  A      CG1 <->  126 THR   ( 129-)  A      N      0.11    2.89  INTRA BF
 498 GLN   ( 129-)  D      NE2 <->  595 LYS   ( 226-)  D      CB     0.10    3.00  INTRA
 234 ARG   (  55-)  B      N   <->  235 PRO   (  56-)  B      CD     0.10    2.90  INTRA
And so on for a total of 79 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

  97 ARG   ( 100-)  A      -6.48
 606 LYS   ( 237-)  D      -5.88
 368 ARG   ( 189-)  B      -5.87
 290 HIS   ( 111-)  B      -5.80
 289 GLN   ( 110-)  B      -5.61
 345 ARG   ( 166-)  B      -5.56
 447 LEU   (  69-)  D      -5.30
 607 ASN   ( 238-)  D      -5.14
 560 ASN   ( 191-)  D      -5.01

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

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: D

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.

 467 TYR   (  89-)  D     -  470 ASN   (  92-)  D        -1.98

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

Note: Second generation quality Z-score plot

Chain identifier: D

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.

 616 HOH   ( 347 )  D      O    -39.83   67.29  -22.82

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.

  81 ASN   (  84-)  A
 140 HIS   ( 143-)  A
 189 GLN   (  10-)  B
 313 ASN   ( 134-)  B
 466 ASN   (  88-)  D
 487 HIS   ( 118-)  D
 490 ASN   ( 121-)  D
 498 GLN   ( 129-)  D
 510 ASN   ( 141-)  D
 517 GLN   ( 148-)  D
 526 GLN   ( 157-)  D
 602 HIS   ( 233-)  D

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.

  42 LEU   (  45-)  A      N
  50 SER   (  53-)  A      N
  73 ARG   (  76-)  A      NH2
  95 GLU   (  98-)  A      N
  97 ARG   ( 100-)  A      NH1
 100 ASN   ( 103-)  A      ND2
 118 TRP   ( 121-)  A      NE1
 185 ARG   (   6-)  B      NH1
 185 ARG   (   6-)  B      NH2
 212 ASN   (  33-)  B      N
 214 GLU   (  35-)  B      N
 225 GLU   (  46-)  B      N
 245 ASP   (  66-)  B      N
 329 ASN   ( 150-)  B      ND2
 397 GLY   (  19-)  D      N
 399 MET   (  21-)  D      N
 425 TRP   (  47-)  D      N
 448 ASN   (  70-)  D      N
 474 SER   (  96-)  D      N
 496 ASN   ( 127-)  D      N
 543 TYR   ( 174-)  D      N
 564 THR   ( 195-)  D      N
 588 ASP   ( 219-)  D      N
 605 THR   ( 236-)  D      OG1

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.

   8 GLU   (  11-)  A      OE1
  63 ASP   (  66-)  A      OD2
 146 HIS   ( 149-)  A      ND1

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.

 613 HOH   ( 194 )  A      O  1.15  K  4
 613 HOH   ( 216 )  A      O  1.02  K  4
 613 HOH   ( 239 )  A      O  1.09  K  4 Ion-B
 614 HOH   ( 206 )  B      O  1.11  K  4
 614 HOH   ( 221 )  B      O  0.90  K  4
 614 HOH   ( 254 )  B      O  1.02  K  4 Ion-B
 616 HOH   ( 255 )  D      O  1.15  K  4
 616 HOH   ( 278 )  D      O  1.04  K  4

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.

  18 GLU   (  21-)  A   H-bonding suggests Gln
  63 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
  98 GLU   ( 101-)  A   H-bonding suggests Gln
 159 ASP   ( 162-)  A   H-bonding suggests Asn
 178 ASP   ( 181-)  A   H-bonding suggests Asn
 426 ASP   (  48-)  D   H-bonding suggests Asn
 440 ASP   (  62-)  D   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 :  -0.020
  2nd generation packing quality :  -1.287
  Ramachandran plot appearance   :  -0.866
  chi-1/chi-2 rotamer normality  :  -1.354
  Backbone conformation          :  -0.466

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.286 (tight)
  Bond angles                    :   0.625 (tight)
  Omega angle restraints         :   0.267 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.595
  B-factor distribution          :   0.507
  Inside/Outside distribution    :   1.048

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.286 (tight)
  Bond angles                    :   0.625 (tight)
  Omega angle restraints         :   0.267 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.595
  B-factor distribution          :   0.507
  Inside/Outside distribution    :   1.048
==============

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.