WHAT IF Check report

This file was created 2011-12-16 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 pdb1mz5.ent

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'.

  23 SER   (  23-)  A      OG
  28 ARG   (  28-)  A      CG
  28 ARG   (  28-)  A      CD
  28 ARG   (  28-)  A      NE
  28 ARG   (  28-)  A      CZ
  28 ARG   (  28-)  A      NH1
  28 ARG   (  28-)  A      NH2
  31 VAL   (  31-)  A      CG1
  31 VAL   (  31-)  A      CG2
 123 GLN   ( 123-)  A      CG
 123 GLN   ( 123-)  A      CD
 123 GLN   ( 123-)  A      OE1
 123 GLN   ( 123-)  A      NE2
 125 ARG   ( 125-)  A      CG
 125 ARG   ( 125-)  A      CD
 125 ARG   ( 125-)  A      NE
 125 ARG   ( 125-)  A      CZ
 125 ARG   ( 125-)  A      NH1
 125 ARG   ( 125-)  A      NH2
 156 LYS   ( 156-)  A      CG
 156 LYS   ( 156-)  A      CD
 156 LYS   ( 156-)  A      CE
 156 LYS   ( 156-)  A      NZ
 167 GLU   ( 167-)  A      CG
 167 GLU   ( 167-)  A      CD
 167 GLU   ( 167-)  A      OE1
 167 GLU   ( 167-)  A      OE2
 391 ASN   ( 391-)  A      CG
 391 ASN   ( 391-)  A      OD1
 391 ASN   ( 391-)  A      ND2
 535 GLU   ( 541-)  A      CG
 535 GLU   ( 541-)  A      CD
 535 GLU   ( 541-)  A      OE1
 535 GLU   ( 541-)  A      OE2
 539 LYS   ( 545-)  A      CG
 539 LYS   ( 545-)  A      CD
 539 LYS   ( 545-)  A      CE
 539 LYS   ( 545-)  A      NZ
 622 ASP   ( 631-)  A      CG
 622 ASP   ( 631-)  A      OD1
 622 ASP   ( 631-)  A      OD2

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

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.

  36 ARG   (  36-)  A
  88 ARG   (  88-)  A
 251 ARG   ( 251-)  A
 252 ARG   ( 252-)  A
 384 ARG   ( 384-)  A
 432 ARG   ( 438-)  A
 469 ARG   ( 475-)  A
 549 ARG   ( 555-)  A

Warning: Tyrosine convention problem

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

  55 TYR   (  55-)  A
  70 TYR   (  70-)  A
 108 TYR   ( 108-)  A
 193 TYR   ( 193-)  A
 470 TYR   ( 476-)  A
 513 TYR   ( 519-)  A
 523 TYR   ( 529-)  A
 540 TYR   ( 546-)  A
 580 TYR   ( 586-)  A

Warning: Phenylalanine convention problem

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

  11 PHE   (  11-)  A
  35 PHE   (  35-)  A
 114 PHE   ( 114-)  A
 168 PHE   ( 168-)  A
 205 PHE   ( 205-)  A
 227 PHE   ( 227-)  A
 372 PHE   ( 372-)  A
 417 PHE   ( 423-)  A
 450 PHE   ( 456-)  A
 472 PHE   ( 478-)  A
 579 PHE   ( 585-)  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.

  60 ASP   (  60-)  A
  74 ASP   (  74-)  A
 169 ASP   ( 169-)  A
 213 ASP   ( 213-)  A
 214 ASP   ( 214-)  A
 248 ASP   ( 248-)  A
 259 ASP   ( 259-)  A
 316 ASP   ( 316-)  A
 324 ASP   ( 324-)  A
 351 ASP   ( 351-)  A
 505 ASP   ( 511-)  A
 548 ASP   ( 554-)  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.

   9 GLU   (   9-)  A
  22 GLU   (  22-)  A
  29 GLU   (  29-)  A
 256 GLU   ( 256-)  A
 296 GLU   ( 296-)  A
 339 GLU   ( 339-)  A
 358 GLU   ( 358-)  A
 428 GLU   ( 434-)  A
 487 GLU   ( 493-)  A
 501 GLU   ( 507-)  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.

 322 MET   ( 322-)  A      SD   CE    1.46   -5.6
 618 MET   ( 627-)  A      SD   CE    1.53   -4.5
 622 ASP   ( 631-)  A      CA   CB    1.64    5.5

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

 |  0.998695  0.000082  0.000228|
 |  0.000082  0.999299 -0.000603|
 |  0.000228 -0.000603  0.998358|
Proposed new scale matrix

 |  0.013149 -0.000001 -0.000003|
 |  0.000000  0.010713  0.000006|
 | -0.000002  0.000006  0.009496|
With corresponding cell

    A    =  76.050  B   =  93.349  C    = 105.312
    Alpha=  90.069  Beta=  89.974  Gamma=  89.996

The CRYST1 cell dimensions

    A    =  76.150  B   =  93.410  C    = 105.480
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 33.419
(Under-)estimated Z-score: 4.260

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.

  17 THR   (  17-)  A      N    CA   CB  102.80   -4.5
  26 THR   (  26-)  A      CG2  CB   OG1 101.21   -4.0
  52 ASP   (  52-)  A      C    CA   CB  102.24   -4.1
  57 THR   (  57-)  A      CG2  CB   OG1 100.42   -4.4
 124 HIS   ( 124-)  A      CG   ND1  CE1 109.77    4.2
 194 PRO   ( 194-)  A      N    CA   C   100.91   -4.4
 317 ARG   ( 317-)  A      CG   CD   NE  102.72   -4.6
 505 ASP   ( 511-)  A      N    CA   CB   99.69   -6.4
 505 ASP   ( 511-)  A      C    CA   CB   99.66   -5.5
 536 LEU   ( 542-)  A      C    CA   CB  100.87   -4.9
 541 HIS   ( 547-)  A      CG   ND1  CE1 109.80    4.2
 584 PRO   ( 590-)  A      CA   C    O   110.15   -6.3

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.

   9 GLU   (   9-)  A
  22 GLU   (  22-)  A
  29 GLU   (  29-)  A
  36 ARG   (  36-)  A
  60 ASP   (  60-)  A
  74 ASP   (  74-)  A
  88 ARG   (  88-)  A
 169 ASP   ( 169-)  A
 213 ASP   ( 213-)  A
 214 ASP   ( 214-)  A
 248 ASP   ( 248-)  A
 251 ARG   ( 251-)  A
 252 ARG   ( 252-)  A
 256 GLU   ( 256-)  A
 259 ASP   ( 259-)  A
 296 GLU   ( 296-)  A
 316 ASP   ( 316-)  A
 324 ASP   ( 324-)  A
 339 GLU   ( 339-)  A
 351 ASP   ( 351-)  A
 358 GLU   ( 358-)  A
 384 ARG   ( 384-)  A
 428 GLU   ( 434-)  A
 432 ARG   ( 438-)  A
 469 ARG   ( 475-)  A
 487 GLU   ( 493-)  A
 501 GLU   ( 507-)  A
 505 ASP   ( 511-)  A
 548 ASP   ( 554-)  A
 549 ARG   ( 555-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 505 ASP   ( 511-)  A      CA     7.1    47.85    33.73
The average deviation= 1.265

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.

 194 PRO   ( 194-)  A    4.86
 184 ILE   ( 184-)  A    4.46
 529 SER   ( 535-)  A    4.30
  64 ILE   (  64-)  A    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.

 276 THR   ( 276-)  A    -2.9
  77 THR   (  77-)  A    -2.7
 132 PRO   ( 132-)  A    -2.7
  37 ILE   (  37-)  A    -2.7
 147 LYS   ( 147-)  A    -2.5
  57 THR   (  57-)  A    -2.5
 145 ASN   ( 145-)  A    -2.5
 273 HIS   ( 273-)  A    -2.5
 334 ILE   ( 334-)  A    -2.4
 235 LEU   ( 235-)  A    -2.3
 219 LYS   ( 219-)  A    -2.3
 290 PHE   ( 290-)  A    -2.3
 448 LEU   ( 454-)  A    -2.3
 177 VAL   ( 177-)  A    -2.3
 250 ASN   ( 250-)  A    -2.2
 531 THR   ( 537-)  A    -2.2
 296 GLU   ( 296-)  A    -2.2
 347 LEU   ( 347-)  A    -2.2
 260 MET   ( 260-)  A    -2.2
 491 GLY   ( 497-)  A    -2.2
 569 ARG   ( 575-)  A    -2.1
 281 SER   ( 281-)  A    -2.1
 583 GLY   ( 589-)  A    -2.1
 141 LYS   ( 141-)  A    -2.1
 356 LEU   ( 356-)  A    -2.1

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.

  37 ILE   (  37-)  A  Poor phi/psi
  74 ASP   (  74-)  A  Poor phi/psi
  88 ARG   (  88-)  A  Poor phi/psi
  95 VAL   (  95-)  A  omega poor
  97 ASP   (  97-)  A  Poor phi/psi
  99 THR   (  99-)  A  omega poor
 142 SER   ( 142-)  A  Poor phi/psi
 143 ALA   ( 143-)  A  Poor phi/psi
 144 ALA   ( 144-)  A  Poor phi/psi
 180 VAL   ( 180-)  A  Poor phi/psi
 183 ALA   ( 183-)  A  Poor phi/psi
 184 ILE   ( 184-)  A  omega poor
 214 ASP   ( 214-)  A  Poor phi/psi
 231 GLU   ( 231-)  A  Poor phi/psi
 267 ALA   ( 267-)  A  Poor phi/psi
 273 HIS   ( 273-)  A  Poor phi/psi
 278 SER   ( 278-)  A  Poor phi/psi
 281 SER   ( 281-)  A  Poor phi/psi
 308 ASN   ( 308-)  A  Poor phi/psi
 312 ARG   ( 312-)  A  Poor phi/psi
 317 ARG   ( 317-)  A  Poor phi/psi
 325 ASN   ( 325-)  A  Poor phi/psi
 341 SER   ( 341-)  A  Poor phi/psi
 351 ASP   ( 351-)  A  Poor phi/psi
 358 GLU   ( 358-)  A  omega poor
 363 ASP   ( 363-)  A  Poor phi/psi
 369 PHE   ( 369-)  A  omega poor
 419 SER   ( 425-)  A  Poor phi/psi
 432 ARG   ( 438-)  A  Poor phi/psi
 446 ASN   ( 452-)  A  Poor phi/psi
 461 VAL   ( 467-)  A  Poor phi/psi
 483 VAL   ( 489-)  A  omega poor
 504 GLY   ( 510-)  A  omega poor
 517 ARG   ( 523-)  A  Poor phi/psi
 537 HIS   ( 543-)  A  Poor phi/psi
 549 ARG   ( 555-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.029

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 PRO   (   3-)  A      0
   5 SER   (   5-)  A      0
   6 SER   (   6-)  A      0
  13 ARG   (  13-)  A      0
  14 LYS   (  14-)  A      0
  15 ASN   (  15-)  A      0
  16 SER   (  16-)  A      0
  33 HIS   (  33-)  A      0
  36 ARG   (  36-)  A      0
  37 ILE   (  37-)  A      0
  38 PRO   (  38-)  A      0
  56 GLU   (  56-)  A      0
  57 THR   (  57-)  A      0
  62 SER   (  62-)  A      0
  63 PHE   (  63-)  A      0
  72 VAL   (  72-)  A      0
  74 ASP   (  74-)  A      0
  76 ALA   (  76-)  A      0
  77 THR   (  77-)  A      0
  83 ALA   (  83-)  A      0
  87 SER   (  87-)  A      0
  88 ARG   (  88-)  A      0
  89 ALA   (  89-)  A      0
  93 SER   (  93-)  A      0
  95 VAL   (  95-)  A      0
And so on for a total of 295 lines.

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]

 402 PRO   ( 402-)  A    0.17 LOW
 460 PRO   ( 466-)  A    0.06 LOW
 530 PRO   ( 536-)  A    0.13 LOW
 587 PRO   ( 596-)  A    0.47 HIGH

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].

 132 PRO   ( 132-)  A   -18.1 half-chair C-alpha/N (-18 degrees)
 494 PRO   ( 500-)  A    14.3 half-chair N/C-delta (18 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.

 259 ASP   ( 259-)  A      OD2 <->  263 THR   ( 263-)  A      CG2    0.62    2.18  INTRA
  17 THR   (  17-)  A      CG2 <->   29 GLU   (  29-)  A      OE1    0.57    2.23  INTRA
 391 ASN   ( 391-)  A      CB  <->  628 HOH   ( 995 )  A      O      0.55    2.25  INTRA
 349 LYS   ( 349-)  A      NZ  <->  350 ASP   ( 350-)  A      OD2    0.41    2.29  INTRA
 168 PHE   ( 168-)  A      O   <->  171 ILE   ( 171-)  A      N      0.37    2.33  INTRA
 537 HIS   ( 543-)  A      CD2 <->  628 HOH   ( 821 )  A      O      0.33    2.47  INTRA BL
  24 ASN   (  24-)  A      OD1 <->   26 THR   (  26-)  A      CG2    0.28    2.52  INTRA BF
 610 ARG   ( 619-)  A      NH1 <->  628 HOH   ( 871 )  A      O      0.28    2.42  INTRA
 167 GLU   ( 167-)  A      CB  <->  628 HOH   ( 913 )  A      O      0.28    2.52  INTRA
 581 ILE   ( 587-)  A      CD1 <->  597 ILE   ( 606-)  A      CD1    0.27    2.93  INTRA BL
 615 SER   ( 624-)  A      CB  <->  618 MET   ( 627-)  A      CE     0.24    2.96  INTRA
 355 SER   ( 355-)  A      CB  <->  372 PHE   ( 372-)  A      CZ     0.22    2.98  INTRA
 627 NAG   ( 655-)  A      O6  <->  628 HOH   ( 936 )  A      O      0.21    2.19  INTRA
  26 THR   (  26-)  A      CG2 <->  624 NAG   ( 652-)  A      C1     0.21    2.99  INTRA BF
 144 ALA   ( 144-)  A      O   <->  146 GLY   ( 146-)  A      N      0.20    2.50  INTRA BF
 482 THR   ( 488-)  A      OG1 <->  616 GLN   ( 625-)  A      NE2    0.20    2.50  INTRA BL
 360 ASN   ( 360-)  A      ND2 <->  363 ASP   ( 363-)  A      N      0.20    2.65  INTRA BL
 199 ASP   ( 199-)  A      OD2 <->  203 ARG   ( 203-)  A      NE     0.19    2.51  INTRA
 207 LYS   ( 207-)  A      NZ  <->  223 GLY   ( 223-)  A      O      0.16    2.54  INTRA BL
 161 LYS   ( 161-)  A      N   <->  162 PRO   ( 162-)  A      CD     0.16    2.84  INTRA
 425 SER   ( 431-)  A      OG  <->  626 NAG   ( 654-)  A      C8     0.15    2.65  INTRA
 520 ARG   ( 526-)  A      NH2 <->  628 HOH   ( 945 )  A      O      0.15    2.55  INTRA
 143 ALA   ( 143-)  A      CB  <->  148 THR   ( 148-)  A      CA     0.15    3.05  INTRA BF
 558 GLN   ( 564-)  A      NE2 <->  628 HOH   ( 848 )  A      O      0.14    2.56  INTRA
 259 ASP   ( 259-)  A      CG  <->  263 THR   ( 263-)  A      CG2    0.14    3.06  INTRA
And so on for a total of 102 lines.

Packing, accessibility and threading

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.

 569 ARG   ( 575-)  A      -8.09
 443 ARG   ( 449-)  A      -6.30
 200 MET   ( 200-)  A      -5.79
 463 ARG   ( 469-)  A      -5.55
 490 LYS   ( 496-)  A      -5.54
 464 GLN   ( 470-)  A      -5.39
 118 ARG   ( 118-)  A      -5.33
 400 VAL   ( 400-)  A      -5.08

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.

 400 VAL   ( 400-)  A       403 - ALA    403- ( A)         -4.46

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.

  28 ARG   (  28-)  A   -3.27
 125 ARG   ( 125-)  A   -2.50

Warning: Abnormal packing Z-score for sequential residues

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

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

 311 GLY   ( 311-)  A     -  314 MET   ( 314-)  A        -1.72
 469 ARG   ( 475-)  A     -  472 PHE   ( 478-)  A        -1.65

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.

 628 HOH   ( 768 )  A      O
 628 HOH   ( 917 )  A      O
 628 HOH   ( 973 )  A      O
Bound group on Asn; dont flip   15 ASN  (  15-) A
Bound to:  623 NAG  ( 651-) A
Bound group on Asn; dont flip   24 ASN  (  24-) A
Bound to:  624 NAG  ( 652-) A
Bound group on Asn; dont flip  115 ASN  ( 115-) A
Bound to:  625 NAG  ( 653-) A
Bound group on Asn; dont flip  423 ASN  ( 429-) A
Bound to:  626 NAG  ( 654-) A
Bound group on Asn; dont flip  605 ASN  ( 614-) A
Bound to:  627 NAG  ( 655-) A

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.

  61 ASN   (  61-)  A
  86 ASN   (  86-)  A
 124 HIS   ( 124-)  A
 196 GLN   ( 196-)  A
 250 ASN   ( 250-)  A
 277 ASN   ( 277-)  A
 284 GLN   ( 284-)  A
 360 ASN   ( 360-)  A
 541 HIS   ( 547-)  A
 596 ASN   ( 605-)  A
 616 GLN   ( 625-)  A

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  62 SER   (  62-)  A      N
  86 ASN   (  86-)  A      ND2
 122 THR   ( 122-)  A      N
 149 THR   ( 149-)  A      N
 176 PHE   ( 176-)  A      N
 244 ASN   ( 244-)  A      ND2
 245 ASN   ( 245-)  A      ND2
 253 LEU   ( 253-)  A      N
 275 TRP   ( 275-)  A      NE1
 278 SER   ( 278-)  A      N
 313 TRP   ( 313-)  A      N
 316 ASP   ( 316-)  A      N
 325 ASN   ( 325-)  A      ND2
 464 GLN   ( 470-)  A      NE2
 602 ARG   ( 611-)  A      N
 619 ILE   ( 628-)  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.

 175 GLU   ( 175-)  A      OE1

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.

 628 HOH   ( 662 )  A      O  0.91  K  4
 628 HOH   ( 693 )  A      O  1.12  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.

  73 ASP   (  73-)  A   H-bonding suggests Asn; but Alt-Rotamer
 213 ASP   ( 213-)  A   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 :   0.056
  2nd generation packing quality :  -1.001
  Ramachandran plot appearance   :  -0.305
  chi-1/chi-2 rotamer normality  :  -2.029
  Backbone conformation          :  -0.351

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.686
  Bond angles                    :   0.918
  Omega angle restraints         :   0.938
  Side chain planarity           :   0.708
  Improper dihedral distribution :   1.068
  B-factor distribution          :   0.613
  Inside/Outside distribution    :   0.985

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.686
  Bond angles                    :   0.918
  Omega angle restraints         :   0.938
  Side chain planarity           :   0.708
  Improper dihedral distribution :   1.068
  B-factor distribution          :   0.613
  Inside/Outside distribution    :   0.985
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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    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,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      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,
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    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.