WHAT IF Check report

This file was created 2013-12-09 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 pdb3s3j.ent

Checks that need to be done early-on in validation

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.

 662 02Y   ( 278-)  B  -
 663 PHQ   ( 277-)  B  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 276 CYS   ( 277-)  A  -   SG   662 02Y   ( 278-)  B  -   C6

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 176 ASN   ( 177-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 176 ASN   ( 177-)  A  -

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.

 651 VAL   ( 279-)  B  -   N   bound to  662 02Y   ( 278-)  B  -   C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: 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'.

  27 ARG   (  28-)  A      CG
  27 ARG   (  28-)  A      CD
  27 ARG   (  28-)  A      NE
  27 ARG   (  28-)  A      CZ
  27 ARG   (  28-)  A      NH1
  27 ARG   (  28-)  A      NH2
  29 LYS   (  30-)  A      CG
  29 LYS   (  30-)  A      CD
  29 LYS   (  30-)  A      CE
  29 LYS   (  30-)  A      NZ
  69 GLU   (  70-)  A      CG
  69 GLU   (  70-)  A      CD
  69 GLU   (  70-)  A      OE1
  69 GLU   (  70-)  A      OE2
  96 ASP   (  97-)  A      CG
  96 ASP   (  97-)  A      OD1
  96 ASP   (  97-)  A      OD2
 124 TYR   ( 125-)  A      CG
 124 TYR   ( 125-)  A      CD1
 124 TYR   ( 125-)  A      CD2
 124 TYR   ( 125-)  A      CE1
 124 TYR   ( 125-)  A      CE2
 124 TYR   ( 125-)  A      CZ
 124 TYR   ( 125-)  A      OH
 230 ASN   ( 231-)  A      CG
And so on for a total of 120 lines.

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.

   2 GLU   (   3-)  A    High
 304 HIS   ( 305-)  A    High
 435 HIS   ( 461-)  A    High
 624 MET   ( 659-)  A    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

Nomenclature related problems

Warning: Tyrosine convention problem

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

 310 TYR   ( 315-)  A
 369 TYR   ( 388-)  A
 419 TYR   ( 445-)  A
 468 TYR   ( 503-)  A
 493 TYR   ( 528-)  A

Warning: Phenylalanine convention problem

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

  38 PHE   (  39-)  A
  44 PHE   (  45-)  A
  58 PHE   (  59-)  A
  76 PHE   (  77-)  A
 129 PHE   ( 130-)  A
 165 PHE   ( 166-)  A
 173 PHE   ( 174-)  A
 202 PHE   ( 203-)  A
 311 PHE   ( 316-)  A
 373 PHE   ( 392-)  A
 502 PHE   ( 537-)  A
 587 PHE   ( 622-)  A
 633 PHE   ( 668-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  24 ASP   (  25-)  A
  54 ASP   (  55-)  A
 190 ASP   ( 191-)  A
 209 ASP   ( 210-)  A
 241 ASP   ( 242-)  A
 258 ASP   ( 259-)  A
 408 ASP   ( 434-)  A
 546 ASP   ( 581-)  A
 618 ASP   ( 653-)  A
 636 ASP   ( 671-)  A

Warning: Glutamic acid convention problem

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

   3 GLU   (   4-)  A
   7 GLU   (   8-)  A
  28 GLU   (  29-)  A
  84 GLU   (  85-)  A
 152 GLU   ( 153-)  A
 154 GLU   ( 155-)  A
 338 GLU   ( 352-)  A
 362 GLU   ( 381-)  A
 421 GLU   ( 447-)  A
 425 GLU   ( 451-)  A
 504 GLU   ( 539-)  A
 534 GLU   ( 569-)  A
 544 GLU   ( 579-)  A
 550 GLU   ( 585-)  A
 561 GLU   ( 596-)  A
 571 GLU   ( 606-)  A
 590 GLU   ( 625-)  A
 608 GLU   ( 643-)  A
 634 GLU   ( 669-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 652 PRO   ( 280-)  B      CA   CB    1.44   -4.3
 652 PRO   ( 280-)  B      N   -C     1.48    7.7
 653 LEU   ( 281-)  B      C    O     1.37    7.1
 653 LEU   ( 281-)  B      N   -C     1.46    6.6

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

 |  0.998229  0.000059 -0.000264|
 |  0.000059  0.999444 -0.000747|
 | -0.000264 -0.000747  0.999200|
Proposed new scale matrix

 |  0.013823  0.000000  0.000004|
 |  0.000000  0.013807  0.000010|
 |  0.000000  0.000002  0.003163|
With corresponding cell

    A    =  72.341  B   =  72.429  C    = 316.203
    Alpha=  90.086  Beta=  90.017  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  72.470  B   =  72.470  C    = 316.461
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 29.357
(Under-)estimated Z-score: 3.993

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.

   3 GLU   (   4-)  A
   7 GLU   (   8-)  A
  24 ASP   (  25-)  A
  28 GLU   (  29-)  A
  54 ASP   (  55-)  A
  84 GLU   (  85-)  A
 152 GLU   ( 153-)  A
 154 GLU   ( 155-)  A
 190 ASP   ( 191-)  A
 209 ASP   ( 210-)  A
 241 ASP   ( 242-)  A
 258 ASP   ( 259-)  A
 338 GLU   ( 352-)  A
 362 GLU   ( 381-)  A
 408 ASP   ( 434-)  A
 421 GLU   ( 447-)  A
 425 GLU   ( 451-)  A
 504 GLU   ( 539-)  A
 534 GLU   ( 569-)  A
 544 GLU   ( 579-)  A
 546 ASP   ( 581-)  A
 550 GLU   ( 585-)  A
 561 GLU   ( 596-)  A
 571 GLU   ( 606-)  A
 590 GLU   ( 625-)  A
 608 GLU   ( 643-)  A
 618 ASP   ( 653-)  A
 634 GLU   ( 669-)  A
 636 ASP   ( 671-)  A

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.

 537 ILE   ( 572-)  A    -2.6
  40 LEU   (  41-)  A    -2.5
 316 MET   ( 330-)  A    -2.4
 499 LEU   ( 534-)  A    -2.4
 534 GLU   ( 569-)  A    -2.3
 579 PRO   ( 614-)  A    -2.3
 577 PRO   ( 612-)  A    -2.2
 345 PRO   ( 359-)  A    -2.2
 591 GLY   ( 626-)  A    -2.1
  90 THR   (  91-)  A    -2.1
 544 GLU   ( 579-)  A    -2.1
 562 PRO   ( 597-)  A    -2.1
 558 ILE   ( 593-)  A    -2.1
 402 THR   ( 428-)  A    -2.1
 622 LEU   ( 657-)  A    -2.1
 502 PHE   ( 537-)  A    -2.1
 147 VAL   ( 148-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  21 HIS   (  22-)  A  Poor phi/psi
  27 ARG   (  28-)  A  Poor phi/psi
  38 PHE   (  39-)  A  omega poor
  86 ASP   (  87-)  A  omega poor
  95 GLN   (  96-)  A  Poor phi/psi
 168 GLN   ( 169-)  A  Poor phi/psi
 213 ARG   ( 214-)  A  Poor phi/psi
 229 CYS   ( 230-)  A  Poor phi/psi
 230 ASN   ( 231-)  A  Poor phi/psi
 232 ASP   ( 233-)  A  Poor phi/psi
 234 GLY   ( 235-)  A  omega poor
 242 ASN   ( 243-)  A  Poor phi/psi
 268 CYS   ( 269-)  A  Poor phi/psi
 272 LYS   ( 273-)  A  omega poor
 274 GLY   ( 275-)  A  omega poor
 323 TRP   ( 337-)  A  Poor phi/psi
 349 THR   ( 368-)  A  Poor phi/psi
 353 GLY   ( 372-)  A  PRO omega poor
 364 ASP   ( 383-)  A  omega poor
 368 LYS   ( 387-)  A  omega poor
 370 ASP   ( 389-)  A  Poor phi/psi
 400 ILE   ( 426-)  A  omega poor
 408 ASP   ( 434-)  A  Poor phi/psi
 455 ASP   ( 490-)  A  omega poor
 457 PHE   ( 492-)  A  omega poor
 524 ASN   ( 559-)  A  Poor phi/psi
 538 ASN   ( 573-)  A  Poor phi/psi
 565 LYS   ( 600-)  A  Poor phi/psi
 622 LEU   ( 657-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.005

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.005

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 ARG   (   9-)  A      0
  21 HIS   (  22-)  A      0
  22 THR   (  23-)  A      0
  26 CYS   (  27-)  A      0
  27 ARG   (  28-)  A      0
  28 GLU   (  29-)  A      0
  34 ARG   (  35-)  A      0
  39 TRP   (  40-)  A      0
  45 GLU   (  46-)  A      0
  47 ARG   (  48-)  A      0
  49 TYR   (  50-)  A      0
  53 VAL   (  54-)  A      0
  62 THR   (  63-)  A      0
  64 PRO   (  65-)  A      0
  65 ALA   (  66-)  A      0
  66 PRO   (  67-)  A      0
  72 THR   (  73-)  A      0
  79 ARG   (  80-)  A      0
  81 ALA   (  82-)  A      0
  84 GLU   (  85-)  A      0
  87 TRP   (  88-)  A      0
  92 VAL   (  93-)  A      0
  93 ASP   (  94-)  A      0
  95 GLN   (  96-)  A      0
  96 ASP   (  97-)  A      0
And so on for a total of 277 lines.

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!

 591 GLY   ( 626-)  A   1.89   24

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].

 487 PRO   ( 522-)  A  -122.2 half-chair C-delta/C-gamma (-126 degrees)
 535 PRO   ( 570-)  A    48.8 half-chair C-delta/C-gamma (54 degrees)
 577 PRO   ( 612-)  A   -64.8 envelop C-beta (-72 degrees)
 621 PRO   ( 656-)  A  -112.2 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 276 CYS   ( 277-)  A      SG   <->   662 02Y   ( 278-)  B      C6   1.25    1.75  INTRA BL
 651 VAL   ( 279-)  B      N    <->   662 02Y   ( 278-)  B      C1   1.23    1.47  INTRA BL
 662 02Y   ( 278-)  B      N    <->   663 PHQ   ( 277-)  B      C1   1.21    1.49  INTRA BL
 651 VAL   ( 279-)  B      CA   <->   662 02Y   ( 278-)  B      C1   0.67    2.53  INTRA BL
 662 02Y   ( 278-)  B      CA   <->   663 PHQ   ( 277-)  B      C1   0.61    2.39  INTRA BL
 231 ASP   ( 232-)  A      O    <->   233 GLN   ( 234-)  A      N    0.48    2.22  INTRA BF
 276 CYS   ( 277-)  A      CB   <->   662 02Y   ( 278-)  B      C6   0.40    2.80  INTRA BL
 517 ARG   ( 552-)  A      CG   <->   518 ASP   ( 553-)  A      N    0.38    2.62  INTRA BF
 534 GLU   ( 569-)  A      CG   <->   537 ILE   ( 572-)  A      CD1  0.33    2.87  INTRA BF
 391 ASN   ( 417-)  A      OD1  <->   393 SER   ( 419-)  A      N    0.27    2.43  INTRA BF
 371 ALA   ( 390-)  A      N    <->   372 PRO   ( 391-)  A      CD   0.24    2.76  INTRA BL
 228 ASN   ( 229-)  A      ND2  <->   347 PRO   ( 361-)  A      CG   0.22    2.88  INTRA BF
 590 GLU   ( 625-)  A      OE1  <->   598 GLN   ( 633-)  A      NE2  0.20    2.50  INTRA BL
 478 THR   ( 513-)  A      O    <->   486 GLY   ( 521-)  A      N    0.19    2.51  INTRA BF
 407 ARG   ( 433-)  A      N    <->   661 GOL   ( 707-)  A      C3   0.17    2.93  INTRA BF
 165 PHE   ( 166-)  A      CD1  <->   176 ASN   ( 177-)  A    A ND2  0.16    2.94  INTRA BL
 564 GLN   ( 599-)  A      N    <->   650 GLY   ( 685-)  A      C    0.16    2.94  INTRA BF
 349 THR   ( 368-)  A      CG2  <->   350 TYR   ( 369-)  A      N    0.14    2.86  INTRA BF
 149 LEU   ( 150-)  A      O    <->   155 ARG   ( 156-)  A      NH1  0.13    2.57  INTRA BL
 407 ARG   ( 433-)  A      NH2  <->   409 GLU   ( 435-)  A      CG   0.13    2.97  INTRA BF
 514 GLU   ( 549-)  A      N    <->   664 HOH   ( 924 )  A      O    0.13    2.57  INTRA BF
 228 ASN   ( 229-)  A      CG   <->   347 PRO   ( 361-)  A      CG   0.12    3.08  INTRA BF
 228 ASN   ( 229-)  A      CG   <->   229 CYS   ( 230-)  A      N    0.12    2.88  INTRA BF
 531 LEU   ( 566-)  A      CD1  <->   542 LEU   ( 577-)  A      CD2  0.11    3.09  INTRA BF
 513 TYR   ( 548-)  A      O    <->   517 ARG   ( 552-)  A      N    0.11    2.59  INTRA BF
And so on for a total of 83 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

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.

 481 TYR   ( 516-)  A      -7.69
 334 GLN   ( 348-)  A      -6.97
 561 GLU   ( 596-)  A      -6.74
 624 MET   ( 659-)  A      -6.67
 622 LEU   ( 657-)  A      -6.40
 553 GLU   ( 588-)  A      -5.96
 369 TYR   ( 388-)  A      -5.83
  20 HIS   (  21-)  A      -5.74
 368 LYS   ( 387-)  A      -5.45
 623 HIS   ( 658-)  A      -5.37
 265 ASN   ( 266-)  A      -5.24
 434 ASN   ( 460-)  A      -5.18
 649 ILE   ( 684-)  A      -5.15
 575 GLN   ( 610-)  A      -5.12

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.

 622 LEU   ( 657-)  A       624 - MET    659- ( A)         -6.15
 648 ILE   ( 683-)  A       650 - GLY    685- ( A)         -4.59

Note: Quality value plot

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

Chain identifier: A

Warning: Low packing Z-score for some residues

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

 566 ARG   ( 601-)  A   -3.44
 350 TYR   ( 369-)  A   -3.02
 269 GLN   ( 270-)  A   -2.83
  29 LYS   (  30-)  A   -2.81
  27 ARG   (  28-)  A   -2.81
 124 TYR   ( 125-)  A   -2.78
 649 ILE   ( 684-)  A   -2.75
 392 ARG   ( 418-)  A   -2.68
 230 ASN   ( 231-)  A   -2.58

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.

 562 PRO   ( 597-)  A     -  567 LYS   ( 602-)  A        -2.15

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: 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.

   4 LEU   (   5-)  A      N
  30 LEU   (  31-)  A      N
  36 GLN   (  37-)  A      N
  46 GLY   (  47-)  A      N
  98 THR   (  99-)  A      N
 105 THR   ( 106-)  A      N
 125 GLN   ( 126-)  A      N
 151 SER   ( 152-)  A      N
 163 GLN   ( 164-)  A      N
 169 GLY   ( 170-)  A      N
 206 ALA   ( 207-)  A      N
 240 TRP   ( 241-)  A      NE1
 253 TRP   ( 254-)  A      N
 257 VAL   ( 258-)  A      N
 258 ASP   ( 259-)  A      N
 259 ILE   ( 260-)  A      N
 270 ARG   ( 271-)  A      N
 275 GLN   ( 276-)  A      N
 276 CYS   ( 277-)  A      N
 277 TRP   ( 278-)  A      N
 308 ILE   ( 313-)  A      N
 317 ILE   ( 331-)  A      N
 319 ASN   ( 333-)  A      ND2
 320 PHE   ( 334-)  A      N
 351 CYS   ( 370-)  A      N
 385 TRP   ( 404-)  A      NE1
 394 LEU   ( 420-)  A      N
 403 LYS   ( 429-)  A      NZ
 409 GLU   ( 435-)  A      N
 437 GLY   ( 472-)  A      N
 449 ASN   ( 484-)  A      N
 483 GLY   ( 518-)  A      N
 521 THR   ( 556-)  A      OG1
 525 LEU   ( 560-)  A      N
 565 LYS   ( 600-)  A      N
 580 VAL   ( 615-)  A      N
 585 CYS   ( 620-)  A      N
 605 ASP   ( 640-)  A      N
 622 LEU   ( 657-)  A      N
 623 HIS   ( 658-)  A      N
 640 ALA   ( 675-)  A      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 275 GLN   ( 276-)  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.

 611 GLU   ( 646-)  A   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.637
  2nd generation packing quality :  -2.143
  Ramachandran plot appearance   :  -1.320
  chi-1/chi-2 rotamer normality  :  -3.005 (poor)
  Backbone conformation          :   0.029

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.570 (tight)
  Omega angle restraints         :   0.993
  Side chain planarity           :   0.322 (tight)
  Improper dihedral distribution :   0.593
  B-factor distribution          :   0.870
  Inside/Outside distribution    :   1.032

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 : 2.25


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -2.3
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.570 (tight)
  Omega angle restraints         :   0.993
  Side chain planarity           :   0.322 (tight)
  Improper dihedral distribution :   0.593
  B-factor distribution          :   0.870
  Inside/Outside distribution    :   1.032
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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.