WHAT IF Check report

This file was created 2012-01-19 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 pdb1yom.ent

Checks that need to be done early-on in validation

Warning: Triclinic cell with mixed acute and obtuse angles

The crystallographic unit cell does not conform to the convention that a triclinic cell should be specified as having either three obtuse (type II) or three acute angles (type I).

The CRYST1 cell dimensions

    A    =  41.698  B   =  63.078  C    =  74.055
    Alpha= 100.610  Beta=  88.860  Gamma=  89.890

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    =  41.698  B   =  63.078  C    =  74.055
    Alpha= 100.610  Beta=  88.860  Gamma=  89.890

Dimensions of a reduced cell

    A    =  41.698  B   =  63.078  C    =  74.055
    Alpha= 100.610  Beta=  91.140  Gamma=  90.110

Dimensions of the conventional cell

    A    =  41.698  B   =  63.078  C    =  74.055
    Alpha= 100.610  Beta=  91.140  Gamma=  90.110

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  0.000000 -1.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

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.

 524 P01   (   1-)  A  -
 525 P01   (   2-)  B  -

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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  21 GLN   ( 277-)  A      CB
  21 GLN   ( 277-)  A      CG
  21 GLN   ( 277-)  A      CD
  21 GLN   ( 277-)  A      OE1
  21 GLN   ( 277-)  A      NE2
  56 GLU   ( 312-)  A      CG
  56 GLU   ( 312-)  A      CD
  56 GLU   ( 312-)  A      OE1
  56 GLU   ( 312-)  A      OE2
 151 PHE   ( 426-)  A      CG
 151 PHE   ( 426-)  A      CD1
 151 PHE   ( 426-)  A      CD2
 151 PHE   ( 426-)  A      CE1
 151 PHE   ( 426-)  A      CE2
 151 PHE   ( 426-)  A      CZ
 281 GLN   ( 277-)  B      CB
 281 GLN   ( 277-)  B      CG
 281 GLN   ( 277-)  B      CD
 281 GLN   ( 277-)  B      OE1
 281 GLN   ( 277-)  B      NE2
 301 LYS   ( 297-)  B      CG
 301 LYS   ( 297-)  B      CD
 301 LYS   ( 297-)  B      CE
 301 LYS   ( 297-)  B      NZ
 316 GLU   ( 312-)  B      CG
 316 GLU   ( 312-)  B      CD
 316 GLU   ( 312-)  B      OE1
 316 GLU   ( 312-)  B      OE2
 412 PHE   ( 426-)  B      CG
 412 PHE   ( 426-)  B      CD1
 412 PHE   ( 426-)  B      CD2
 412 PHE   ( 426-)  B      CE1
 412 PHE   ( 426-)  B      CE2
 412 PHE   ( 426-)  B      CZ

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  47 THR   ( 303-)  A    High
  48 MET   ( 304-)  A    High
  49 SER   ( 305-)  A    High
  50 PRO   ( 306-)  A    High
  51 GLU   ( 307-)  A    High
  52 ALA   ( 308-)  A    High
  53 PHE   ( 309-)  A    High
  54 LEU   ( 310-)  A    High
  55 GLN   ( 311-)  A    High
 308 MET   ( 304-)  B    High
 310 PRO   ( 306-)  B    High

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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

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.

  14 ARG   ( 270-)  A
 274 ARG   ( 270-)  B

Warning: Tyrosine convention problem

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

 341 TYR   ( 337-)  B
 382 TYR   ( 378-)  B
 515 TYR   ( 529-)  B

Warning: Phenylalanine convention problem

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

 242 PHE   ( 517-)  A
 427 PHE   ( 441-)  B
 503 PHE   ( 517-)  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.

   4 ASP   ( 260-)  A
 264 ASP   ( 260-)  B
 371 ASP   ( 367-)  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.

  11 GLU   ( 267-)  A
  16 GLU   ( 272-)  A
  26 GLU   ( 282-)  A
  77 GLU   ( 333-)  A
  85 GLU   ( 341-)  A
 197 GLU   ( 472-)  A
 216 GLU   ( 491-)  A
 231 GLU   ( 506-)  A
 251 GLU   ( 526-)  A
 258 GLU   ( 533-)  A
 276 GLU   ( 272-)  B
 286 GLU   ( 282-)  B
 311 GLU   ( 307-)  B
 326 GLU   ( 322-)  B
 345 GLU   ( 341-)  B
 458 GLU   ( 472-)  B
 477 GLU   ( 491-)  B
 492 GLU   ( 506-)  B
 493 GLU   ( 507-)  B
 498 GLU   ( 512-)  B
 512 GLU   ( 526-)  B
 519 GLU   ( 533-)  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

 |  0.997364 -0.000174  0.000786|
 | -0.000174  0.996596  0.000072|
 |  0.000786  0.000072  0.997115|
Proposed new scale matrix

 |  0.024046 -0.000042 -0.000516|
 |  0.000000  0.015907  0.002978|
 | -0.000011 -0.000001  0.013781|
With corresponding cell

    A    =  41.588  B   =  62.865  C    =  73.842
    Alpha= 100.597  Beta=  88.763  Gamma=  89.909

The CRYST1 cell dimensions

    A    =  41.698  B   =  63.078  C    =  74.055
    Alpha= 100.610  Beta=  88.860  Gamma=  89.890

Variance: 155.287
(Under-)estimated Z-score: 9.184

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.

 183 THR   ( 458-)  A      CG2  CB   OG1 100.92   -4.2
 325 HIS   ( 321-)  B      CG   ND1  CE1 109.60    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.

   4 ASP   ( 260-)  A
  11 GLU   ( 267-)  A
  14 ARG   ( 270-)  A
  16 GLU   ( 272-)  A
  26 GLU   ( 282-)  A
  77 GLU   ( 333-)  A
  85 GLU   ( 341-)  A
 197 GLU   ( 472-)  A
 216 GLU   ( 491-)  A
 231 GLU   ( 506-)  A
 251 GLU   ( 526-)  A
 258 GLU   ( 533-)  A
 264 ASP   ( 260-)  B
 274 ARG   ( 270-)  B
 276 GLU   ( 272-)  B
 286 GLU   ( 282-)  B
 311 GLU   ( 307-)  B
 326 GLU   ( 322-)  B
 345 GLU   ( 341-)  B
 371 ASP   ( 367-)  B
 458 GLU   ( 472-)  B
 477 GLU   ( 491-)  B
 492 GLU   ( 506-)  B
 493 GLU   ( 507-)  B
 498 GLU   ( 512-)  B
 512 GLU   ( 526-)  B
 519 GLU   ( 533-)  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.

 436 PHE   ( 450-)  B    4.32

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.989

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.

 307 THR   ( 303-)  B    -3.7
 296 THR   ( 292-)  B    -3.6
  36 THR   ( 292-)  A    -3.0
 152 PRO   ( 427-)  A    -2.9
 413 PRO   ( 427-)  B    -2.9
 305 PRO   ( 301-)  B    -2.8
 473 PRO   ( 487-)  B    -2.8
 274 ARG   ( 270-)  B    -2.6
 212 PRO   ( 487-)  A    -2.5
 446 LYS   ( 460-)  B    -2.5
   3 LYS   ( 259-)  A    -2.5
 337 GLU   ( 333-)  B    -2.5
  47 THR   ( 303-)  A    -2.5
 252 PRO   ( 527-)  A    -2.5
  14 ARG   ( 270-)  A    -2.4
 338 GLU   ( 334-)  B    -2.4
 313 PHE   ( 309-)  B    -2.4
  53 PHE   ( 309-)  A    -2.3
 451 TYR   ( 465-)  B    -2.3
 314 LEU   ( 310-)  B    -2.2
  44 LYS   ( 300-)  A    -2.2
  54 LEU   ( 310-)  A    -2.2
  10 ARG   ( 266-)  A    -2.2
 276 GLU   ( 272-)  B    -2.2
 272 SER   ( 268-)  B    -2.2
 144 LEU   ( 400-)  A    -2.2
 493 GLU   ( 507-)  B    -2.1
  38 VAL   ( 294-)  A    -2.1
 194 VAL   ( 469-)  A    -2.1
 168 ILE   ( 443-)  A    -2.1
 143 ASN   ( 399-)  A    -2.1
 183 THR   ( 458-)  A    -2.1
  11 GLU   ( 267-)  A    -2.1
 213 GLU   ( 488-)  A    -2.0
 471 CYS   ( 485-)  B    -2.0
 336 SER   ( 332-)  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.

   5 ALA   ( 261-)  A  omega poor
  10 ARG   ( 266-)  A  omega poor
  16 GLU   ( 272-)  A  Poor phi/psi
  21 GLN   ( 277-)  A  Poor phi/psi
  28 TRP   ( 284-)  A  omega poor
  33 ASN   ( 289-)  A  Poor phi/psi
  35 THR   ( 291-)  A  Poor phi/psi
  36 THR   ( 292-)  A  Poor phi/psi
  38 VAL   ( 294-)  A  omega poor
  47 THR   ( 303-)  A  Poor phi/psi
  53 PHE   ( 309-)  A  omega poor
  54 LEU   ( 310-)  A  omega poor
  56 GLU   ( 312-)  A  omega poor
  63 LEU   ( 319-)  A  omega poor
  67 LYS   ( 323-)  A  omega poor
  73 ALA   ( 329-)  A  Poor phi/psi
  75 VAL   ( 331-)  A  omega poor
  78 GLU   ( 334-)  A  PRO omega poor
  87 MET   ( 343-)  A  omega poor
 101 GLY   ( 357-)  A  Poor phi/psi
 131 ARG   ( 387-)  A  Poor phi/psi
 143 ASN   ( 399-)  A  Poor phi/psi
 148 VAL   ( 404-)  A  omega poor
 149 ALA   ( 405-)  A  Poor phi/psi, omega poor
 185 LYS   ( 460-)  A  Poor phi/psi, omega poor
And so on for a total of 52 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.397

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.

 118 SER   ( 374-)  A    0.38

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!

   5 ALA   ( 261-)  A      0
   6 TRP   ( 262-)  A      0
  10 ARG   ( 266-)  A      0
  13 LEU   ( 269-)  A      0
  16 GLU   ( 272-)  A      0
  21 GLN   ( 277-)  A      0
  24 PHE   ( 280-)  A      0
  29 MET   ( 285-)  A      0
  32 TRP   ( 288-)  A      0
  33 ASN   ( 289-)  A      0
  35 THR   ( 291-)  A      0
  36 THR   ( 292-)  A      0
  45 PRO   ( 301-)  A      0
  48 MET   ( 304-)  A      0
  53 PHE   ( 309-)  A      0
  54 LEU   ( 310-)  A      0
  55 GLN   ( 311-)  A      0
  64 ARG   ( 320-)  A      0
  65 HIS   ( 321-)  A      0
  70 GLN   ( 326-)  A      0
  72 TYR   ( 328-)  A      0
  77 GLU   ( 333-)  A      0
  78 GLU   ( 334-)  A      0
  79 PRO   ( 335-)  A      0
  80 ILE   ( 336-)  A      0
And so on for a total of 202 lines.

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 7.620

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!

 158 PRO   ( 433-)  A   1.63   21
 419 PRO   ( 433-)  B   1.56   11

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

   3 LYS   ( 259-)  A   1.52

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 215 PRO   ( 490-)  A    0.11 LOW
 517 PRO   ( 531-)  B    0.12 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  50 PRO   ( 306-)  A   101.8 envelop C-beta (108 degrees)
 152 PRO   ( 427-)  A   -52.0 half-chair C-beta/C-alpha (-54 degrees)
 211 PRO   ( 486-)  A  -115.5 envelop C-gamma (-108 degrees)
 212 PRO   ( 487-)  A   133.2 half-chair C-beta/C-alpha (126 degrees)
 234 PRO   ( 509-)  A    26.7 half-chair N/C-delta (18 degrees)
 252 PRO   ( 527-)  A   -64.6 envelop C-beta (-72 degrees)
 305 PRO   ( 301-)  B   113.5 envelop C-beta (108 degrees)
 339 PRO   ( 335-)  B   -52.1 half-chair C-beta/C-alpha (-54 degrees)
 367 PRO   ( 363-)  B    99.9 envelop C-beta (108 degrees)
 413 PRO   ( 427-)  B   -46.0 half-chair C-beta/C-alpha (-54 degrees)
 419 PRO   ( 433-)  B  -116.4 envelop C-gamma (-108 degrees)
 472 PRO   ( 486-)  B  -119.0 half-chair C-delta/C-gamma (-126 degrees)
 473 PRO   ( 487-)  B   111.8 envelop C-beta (108 degrees)
 476 PRO   ( 490-)  B   113.3 envelop C-beta (108 degrees)
 513 PRO   ( 527-)  B   -55.6 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 179 LEU   ( 454-)  A      O   <->  183 THR   ( 458-)  A      OG1    0.49    1.91  INTRA BL
 430 LYS   ( 444-)  B      NZ  <->  494 ARG   ( 508-)  B      O      0.44    2.26  INTRA BL
 254 TYR   ( 529-)  A      OH  <->  522 LEU   ( 535-)  A      O''    0.41    1.99  INTRA BL
 217 SER   ( 492-)  A      OG  <->  251 GLU   ( 526-)  A      OE2    0.28    2.12  INTRA BL
  29 MET   ( 285-)  A      SD  <->   37 ARG   ( 293-)  A      NE     0.22    3.08  INTRA BF
 497 PHE   ( 511-)  B      O   <->  501 GLN   ( 515-)  B      N      0.22    2.48  INTRA BL
 132 ASP   ( 388-)  A      O   <->  137 ASN   ( 393-)  A      ND2    0.18    2.52  INTRA BL
 390 HIS   ( 386-)  B      N   <->  432 ASP   ( 446-)  B      OD2    0.16    2.54  INTRA BL
 272 SER   ( 268-)  B      O   <->  293 ASN   ( 289-)  B      N      0.16    2.54  INTRA BF
 352 LEU   ( 348-)  B      N   <->  398 ILE   ( 394-)  B      O      0.15    2.55  INTRA BL
 478 SER   ( 492-)  B      OG  <->  512 GLU   ( 526-)  B      OE2    0.14    2.26  INTRA BL
 104 LEU   ( 360-)  A      O   <->  185 LYS   ( 460-)  A      NZ     0.13    2.57  INTRA BL
 435 SER   ( 449-)  B      O   <->  439 LEU   ( 453-)  B      N      0.12    2.58  INTRA BL
 155 TRP   ( 430-)  A      NE1 <->  181 GLU   ( 456-)  A      CD     0.12    2.98  INTRA BL
 272 SER   ( 268-)  B      OG  <->  293 ASN   ( 289-)  B      ND2    0.12    2.58  INTRA BF
 174 SER   ( 449-)  A      O   <->  178 LEU   ( 453-)  A      N      0.11    2.59  INTRA BL
 430 LYS   ( 444-)  B      NZ  <->  527 HOH   ( 549 )  B      O      0.11    2.59  INTRA BL
 414 ILE   ( 428-)  B      CD1 <->  422 ALA   ( 436-)  B      CB     0.10    3.10  INTRA BL
 263 LYS   ( 259-)  B      NZ  <->  337 GLU   ( 333-)  B      OE1    0.10    2.60  INTRA BF
 190 TYR   ( 465-)  A      N   <->  208 MET   ( 483-)  A      SD     0.10    3.20  INTRA BL
 177 ILE   ( 452-)  A      O   <->  180 THR   ( 455-)  A      OG1    0.10    2.30  INTRA BL
 253 GLN   ( 528-)  A      N   <->  526 HOH   ( 567 )  A      O      0.09    2.61  INTRA BL
  87 MET   ( 343-)  A      O   <->  524 P01   (   1-)  A      N6     0.08    2.62  INTRA BL
 105 ARG   ( 361-)  A      NH1 <->  185 LYS   ( 460-)  A      NZ     0.08    2.77  INTRA BL
 457 ARG   ( 471-)  B      O   <->  461 ASP   ( 475-)  B      CG     0.08    2.72  INTRA BL
And so on for a total of 60 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.

  64 ARG   ( 320-)  A      -7.04
 324 ARG   ( 320-)  B      -6.69
 284 PHE   ( 280-)  B      -6.62
 255 GLN   ( 530-)  A      -6.49
 516 GLN   ( 530-)  B      -6.42
 187 ARG   ( 462-)  A      -6.42
 468 ARG   ( 482-)  B      -6.32
  10 ARG   ( 266-)  A      -6.27
 207 ARG   ( 482-)  A      -6.16
 467 TYR   ( 481-)  B      -5.91
 489 LYS   ( 503-)  B      -5.91
 228 LYS   ( 503-)  A      -5.89
 515 TYR   ( 529-)  B      -5.81
 465 ARG   ( 479-)  B      -5.79
 270 ARG   ( 266-)  B      -5.67
 206 TYR   ( 481-)  A      -5.64
 131 ARG   ( 387-)  A      -5.63
 304 LYS   ( 300-)  B      -5.46
  37 ARG   ( 293-)  A      -5.37
 204 ARG   ( 479-)  A      -5.36
 338 GLU   ( 334-)  B      -5.23
 416 TRP   ( 430-)  B      -5.17
 258 GLU   ( 533-)  A      -5.16
 143 ASN   ( 399-)  A      -5.16
  78 GLU   ( 334-)  A      -5.13
 263 LYS   ( 259-)  B      -5.12
 254 TYR   ( 529-)  A      -5.04

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.

   1 LEU   ( 257-)  A         3 - LYS    259- ( A)         -4.28
 206 TYR   ( 481-)  A       208 - MET    483- ( A)         -5.43
 253 GLN   ( 528-)  A       255 - GLN    530- ( A)         -5.24
 514 GLN   ( 528-)  B       516 - GLN    530- ( B)         -5.45

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 521 : -1.540

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.

 281 GLN   ( 277-)  B   -3.52
  21 GLN   ( 277-)  A   -3.51

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

Error: Water molecules without hydrogen bonds

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

 526 HOH   ( 550 )  A      O
 526 HOH   ( 564 )  A      O
 526 HOH   ( 571 )  A      O
 526 HOH   ( 575 )  A      O
 526 HOH   ( 592 )  A      O
 527 HOH   ( 540 )  B      O
 527 HOH   ( 552 )  B      O
 527 HOH   ( 575 )  B      O
 527 HOH   ( 593 )  B      O
 527 HOH   ( 595 )  B      O
 527 HOH   ( 600 )  B      O
Marked this atom as acceptor  524 P01  (   1-) A     CL1
Marked this atom as acceptor  525 P01  (   2-) B     CL1

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.

  58 GLN   ( 314-)  A
 201 GLN   ( 476-)  A
 403 ASN   ( 399-)  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.

   6 TRP   ( 262-)  A      N
  10 ARG   ( 266-)  A      NH1
  11 GLU   ( 267-)  A      N
  13 LEU   ( 269-)  A      N
  17 VAL   ( 273-)  A      N
  25 GLY   ( 281-)  A      N
  32 TRP   ( 288-)  A      NE1
  44 LYS   ( 300-)  A      N
  57 ALA   ( 313-)  A      N
  60 MET   ( 316-)  A      N
  65 HIS   ( 321-)  A      N
  67 LYS   ( 323-)  A      N
  71 LEU   ( 327-)  A      N
  87 MET   ( 343-)  A      N
  88 ASN   ( 344-)  A      N
  93 LEU   ( 349-)  A      N
 132 ASP   ( 388-)  A      N
 134 ARG   ( 390-)  A      N
 155 TRP   ( 430-)  A      N
 155 TRP   ( 430-)  A      NE1
 169 LYS   ( 444-)  A      N
 183 THR   ( 458-)  A      OG1
 196 ARG   ( 471-)  A      N
 233 ARG   ( 508-)  A      N
 265 ALA   ( 261-)  B      N
And so on for a total of 52 lines.

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.

  70 GLN   ( 326-)  A      OE1

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.

 200 ASP   ( 475-)  A   H-bonding suggests Asn
 220 ASP   ( 495-)  A   H-bonding suggests Asn; but Alt-Rotamer
 267 GLU   ( 263-)  B   H-bonding suggests Gln
 276 GLU   ( 272-)  B   H-bonding suggests Gln
 461 ASP   ( 475-)  B   H-bonding suggests Asn
 481 ASP   ( 495-)  B   H-bonding suggests Asn
 512 GLU   ( 526-)  B   H-bonding suggests Gln

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 :  -2.600
  2nd generation packing quality :  -2.448
  Ramachandran plot appearance   :  -3.989 (poor)
  chi-1/chi-2 rotamer normality  :  -4.397 (bad)
  Backbone conformation          :  -0.757

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.642 (tight)
  Bond angles                    :   0.805
  Omega angle restraints         :   1.385 (loose)
  Side chain planarity           :   0.528 (tight)
  Improper dihedral distribution :   0.748
  B-factor distribution          :   0.398
  Inside/Outside distribution    :   1.038

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.5
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.642 (tight)
  Bond angles                    :   0.805
  Omega angle restraints         :   1.385 (loose)
  Side chain planarity           :   0.528 (tight)
  Improper dihedral distribution :   0.748
  B-factor distribution          :   0.398
  Inside/Outside distribution    :   1.038
==============

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.