WHAT IF Check report

This file was created 2012-01-29 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3brd.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 4

Warning: Matthews Coefficient (Vm) high

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

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

Molecular weight of all polymer chains: 59930.832
Volume of the Unit Cell V= 751169.438
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.267
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.830 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 4
which would result in the much more normal Vm= 3.133
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

Warning: Chain identifier inconsistency

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

 481 EDO   (  16-)  A  C

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.

 473 EDO   (   1-)  A  -
 474 EDO   (   2-)  A  -
 475 EDO   (   3-)  A  -
 476 EDO   (   4-)  A  -
 477 EDO   (   5-)  A  -
 478 EDO   (   8-)  A  -
 479 EDO   (   9-)  A  -
 480 EDO   (  10-)  A  -
 481 EDO   (  16-)  A  C
 482 EDO   (   6-)  D  -

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: D

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

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: D

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  40 ARG   ( 234-)  A
 169 ARG   ( 399-)  A
 397 ARG   ( 631-)  A

Warning: Tyrosine convention problem

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

  19 TYR   ( 213-)  A
  35 TYR   ( 229-)  A
  66 TYR   ( 260-)  A
 106 TYR   ( 331-)  A
 115 TYR   ( 340-)  A
 124 TYR   ( 349-)  A
 153 TYR   ( 383-)  A
 177 TYR   ( 407-)  A
 217 TYR   ( 451-)  A
 312 TYR   ( 546-)  A
 416 TYR   ( 650-)  A

Warning: Phenylalanine convention problem

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

  41 PHE   ( 235-)  A
  42 PHE   ( 236-)  A
  93 PHE   ( 304-)  A
 116 PHE   ( 341-)  A
 133 PHE   ( 358-)  A
 195 PHE   ( 425-)  A
 214 PHE   ( 448-)  A
 314 PHE   ( 548-)  A
 352 PHE   ( 586-)  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.

   7 ASP   ( 201-)  A
  84 ASP   ( 295-)  A
  92 ASP   ( 303-)  A
  98 ASP   ( 323-)  A
 117 ASP   ( 342-)  A
 202 ASP   ( 432-)  A
 212 ASP   ( 446-)  A
 225 ASP   ( 459-)  A
 248 ASP   ( 482-)  A
 279 ASP   ( 513-)  A
 298 ASP   ( 532-)  A
 411 ASP   ( 645-)  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.

  38 GLU   ( 232-)  A
 253 GLU   ( 487-)  A
 311 GLU   ( 545-)  A
 335 GLU   ( 569-)  A
 366 GLU   ( 600-)  A
 373 GLU   ( 607-)  A
 388 GLU   ( 622-)  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.

  43 CYS   ( 237-)  A      CB   SG    1.63   -5.5
 358 VAL   ( 592-)  A      CA   CB    1.61    4.0
 441 GLU   ( 950-)  D      C    O     1.32    4.6
 441 GLU   ( 950-)  D      CD   OE1   1.70   23.7
 441 GLU   ( 950-)  D      CD   OE2   1.54   15.5
 442 ASN   ( 951-)  D      CG   OD1   1.47   11.9
 442 ASN   ( 951-)  D      CG   ND2   1.53    9.4
 442 ASN   ( 951-)  D      N   -C     1.42    4.6
 443 DTHY  (   1-)  B      C6   C5    1.37    4.0
 448 DGUA  (   6-)  B      N7   C5    1.41    4.0
 454 DADE  (  12-)  B      N3   C4    1.37    4.1
 458 DADE  (   1-)  C      O5'  C5'   1.52    5.0
 458 DADE  (   1-)  C      C5'  C4'   1.58    8.0
 458 DADE  (   1-)  C      C4'  O4'   1.50    4.8
 458 DADE  (   1-)  C      O4'  C1'   1.50    5.9
 458 DADE  (   1-)  C      C1'  C2'   1.60    5.4
 458 DADE  (   1-)  C      C3'  C2'   1.57    5.0
 458 DADE  (   1-)  C      C5   C4    1.41    4.1
 472 DTHY  (  15-)  C      N1   C6    1.41    4.1
 472 DTHY  (  15-)  C      N1   C2    1.41    4.0

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

 |  0.996737  0.000147  0.000256|
 |  0.000147  0.999945  0.000679|
 |  0.000256  0.000679  0.994299|
Proposed new scale matrix

 |  0.016678 -0.000002 -0.000004|
 | -0.000001  0.010116 -0.000007|
 | -0.000002 -0.000005  0.007962|
With corresponding cell

    A    =  59.958  B   =  98.858  C    = 125.590
    Alpha=  89.922  Beta=  89.971  Gamma=  89.983

The CRYST1 cell dimensions

    A    =  60.153  B   =  98.866  C    = 126.313
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 437.257
(Under-)estimated Z-score: 15.411

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.

  43 CYS   ( 237-)  A      C    CA   CB  102.48   -4.0
 284 HIS   ( 518-)  A      CG   ND1  CE1 109.66    4.1
 339 HIS   ( 573-)  A      CG   ND1  CE1 109.62    4.0
 386 ARG   ( 620-)  A      CB   CG   CD  102.86   -5.6
 386 ARG   ( 620-)  A      CG   CD   NE  118.97    5.0
 410 ARG   ( 644-)  A      CB   CG   CD  104.21   -4.9
 441 GLU   ( 950-)  D      CG   CD   OE2 102.90   -6.7
 442 ASN   ( 951-)  D      CB   CG   ND2 109.18   -4.8
 442 ASN   ( 951-)  D      ND2  CG   OD1 129.51    6.9
 443 DTHY  (   1-)  B      C5   C4   O4  121.85   -4.4
 443 DTHY  (   1-)  B      O4   C4   N3  123.01    5.2
 444 DTHY  (   2-)  B      O4'  C1'  N1  102.76   -6.3
 444 DTHY  (   2-)  B      C2'  C1'  N1  121.12    4.3
 444 DTHY  (   2-)  B      O4   C4   N3  122.42    4.2
 445 DADE  (   3-)  B      P   -C3* -O3* 124.50    4.0
 447 DTHY  (   5-)  B      P   -C3* -O3* 127.93    6.9
 447 DTHY  (   5-)  B      O4'  C1'  N1  103.92   -4.8
 448 DGUA  (   6-)  B      OP1  P    OP2 125.98    4.3
 448 DGUA  (   6-)  B      N9   C8   N7  114.79    7.4
 448 DGUA  (   6-)  B      C8   N9   C4  104.55   -4.6
 448 DGUA  (   6-)  B      C5   C6   N1  114.02    5.0
 449 DTHY  (   7-)  B      C2'  C1'  N1  121.09    4.3
 449 DTHY  (   7-)  B      C6   C5   C7  118.73   -7.0
 449 DTHY  (   7-)  B      C4   C5   C7  122.81    6.4
 450 DGUA  (   8-)  B      O4'  C1'  N9  111.26    4.3
And so on for a total of 62 lines.

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.

   7 ASP   ( 201-)  A
  38 GLU   ( 232-)  A
  40 ARG   ( 234-)  A
  84 ASP   ( 295-)  A
  92 ASP   ( 303-)  A
  98 ASP   ( 323-)  A
 117 ASP   ( 342-)  A
 169 ARG   ( 399-)  A
 202 ASP   ( 432-)  A
 212 ASP   ( 446-)  A
 225 ASP   ( 459-)  A
 248 ASP   ( 482-)  A
 253 GLU   ( 487-)  A
 279 ASP   ( 513-)  A
 298 ASP   ( 532-)  A
 311 GLU   ( 545-)  A
 335 GLU   ( 569-)  A
 366 GLU   ( 600-)  A
 373 GLU   ( 607-)  A
 388 GLU   ( 622-)  A
 397 ARG   ( 631-)  A
 411 ASP   ( 645-)  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.

 221 VAL   ( 455-)  A      CB     6.1   -24.92   -32.96
The average deviation= 1.078

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 441 GLU   ( 950-)  D    7.61

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.

 278 HIS   ( 512-)  A    -2.9
 186 HIS   ( 416-)  A    -2.8
 146 LYS   ( 371-)  A    -2.4
 282 ILE   ( 516-)  A    -2.3
 169 ARG   ( 399-)  A    -2.2
 431 ILE   ( 940-)  D    -2.2
 261 LYS   ( 495-)  A    -2.2
 277 SER   ( 511-)  A    -2.1
  65 LEU   ( 259-)  A    -2.1
 170 SER   ( 400-)  A    -2.1
 246 ILE   ( 480-)  A    -2.1
   2 GLN   ( 196-)  A    -2.0
 373 GLU   ( 607-)  A    -2.0
 204 GLU   ( 438-)  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.

   2 GLN   ( 196-)  A  Poor phi/psi
  14 SER   ( 208-)  A  omega poor
  19 TYR   ( 213-)  A  omega poor
  43 CYS   ( 237-)  A  PRO omega poor
  91 LEU   ( 302-)  A  omega poor
 135 SER   ( 360-)  A  omega poor
 170 SER   ( 400-)  A  Poor phi/psi
 183 ASN   ( 413-)  A  Poor phi/psi
 204 GLU   ( 438-)  A  omega poor
 220 VAL   ( 454-)  A  omega poor
 241 ASP   ( 475-)  A  omega poor
 243 GLN   ( 477-)  A  Poor phi/psi
 249 ALA   ( 483-)  A  Poor phi/psi
 250 SER   ( 484-)  A  Poor phi/psi
 259 LEU   ( 493-)  A  Poor phi/psi
 274 LEU   ( 508-)  A  omega poor
 279 ASP   ( 513-)  A  Poor phi/psi
 290 ASN   ( 524-)  A  Poor phi/psi
 296 ILE   ( 530-)  A  Poor phi/psi
 326 SER   ( 560-)  A  PRO omega poor
 351 ASP   ( 585-)  A  Poor phi/psi
 425 LYS   ( 659-)  A  omega poor
 426 SER   ( 660-)  A  Poor phi/psi
 441 GLU   ( 950-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.080

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 : -3.080

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 SER   ( 197-)  A      0
  19 TYR   ( 213-)  A      0
  27 HIS   ( 221-)  A      0
  29 LYS   ( 223-)  A      0
  35 TYR   ( 229-)  A      0
  38 GLU   ( 232-)  A      0
  42 PHE   ( 236-)  A      0
  43 CYS   ( 237-)  A      0
  44 PRO   ( 238-)  A      0
  45 PRO   ( 239-)  A      0
  51 ILE   ( 245-)  A      0
  68 THR   ( 262-)  A      0
  69 LEU   ( 263-)  A      0
  70 GLN   ( 281-)  A      0
  71 GLN   ( 282-)  A      0
  81 ILE   ( 292-)  A      0
  92 ASP   ( 303-)  A      0
  93 PHE   ( 304-)  A      0
  94 PRO   ( 319-)  A      0
  95 ASN   ( 320-)  A      0
  98 ASP   ( 323-)  A      0
 103 LYS   ( 328-)  A      0
 104 THR   ( 329-)  A      0
 105 LEU   ( 330-)  A      0
 124 TYR   ( 349-)  A      0
And so on for a total of 211 lines.

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].

  94 PRO   ( 319-)  A   -48.3 half-chair C-beta/C-alpha (-54 degrees)
 255 PRO   ( 489-)  A    34.7 envelop C-delta (36 degrees)
 405 PRO   ( 639-)  A   -65.2 envelop C-beta (-72 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.

  92 ASP   ( 303-)  A      OD1 <->   93 PHE   ( 304-)  A      N      0.65    1.95  INTRA BF
 261 LYS   ( 495-)  A      CE  <->  303 THR   ( 537-)  A      OG1    0.41    2.39  INTRA BF
 243 GLN   ( 477-)  A      N   <->  483 HOH   ( 703 )  A      O      0.41    2.29  INTRA BF
 284 HIS   ( 518-)  A      ND1 <->  441 GLU   ( 950-)  D      OE1    0.36    2.34  INTRA BL
 204 GLU   ( 438-)  A      OE2 <->  222 LYS   ( 456-)  A      NZ     0.34    2.36  INTRA BF
 445 DADE  (   3-)  B      N1  <->  472 DTHY  (  15-)  C      N3     0.29    2.71  INTRA BF
 454 DADE  (  12-)  B      N1  <->  463 DTHY  (   6-)  C      N3     0.29    2.71  INTRA BL
 457 DADE  (  15-)  B      N1  <->  460 DTHY  (   3-)  C      N3     0.28    2.72  INTRA BF
 455 DADE  (  13-)  B      N1  <->  462 DTHY  (   5-)  C      N3     0.28    2.72  INTRA BL
 261 LYS   ( 495-)  A      NZ  <->  483 HOH   ( 681 )  A      O      0.26    2.44  INTRA BF
  43 CYS   ( 237-)  A      SG  <->  167 ARG   ( 397-)  A      NH2    0.26    3.04  INTRA BF
 137 ARG   ( 362-)  A    A NE  <->  153 TYR   ( 383-)  A      OH     0.24    2.46  INTRA BF
 456 DGUA  (  14-)  B      N1  <->  461 DCYT  (   4-)  C      N3     0.23    2.77  INTRA BF
 451 DGUA  (   9-)  B      N1  <->  466 DCYT  (   9-)  C      N3     0.23    2.77  INTRA BL
 447 DTHY  (   5-)  B      N3  <->  470 DADE  (  13-)  C      N1     0.21    2.79  INTRA BF
 451 DGUA  (   9-)  B      N2  <->  466 DCYT  (   9-)  C      O2     0.21    2.49  INTRA BF
 456 DGUA  (  14-)  B      N2  <->  461 DCYT  (   4-)  C      O2     0.21    2.49  INTRA BF
  92 ASP   ( 303-)  A      CG  <->   93 PHE   ( 304-)  A      N      0.20    2.80  INTRA BF
 450 DGUA  (   8-)  B      N1  <->  467 DCYT  (  10-)  C      N3     0.20    2.80  INTRA BL
 446 DCYT  (   4-)  B      N3  <->  471 DGUA  (  14-)  C      N1     0.20    2.80  INTRA BF
 449 DTHY  (   7-)  B      N3  <->  468 DADE  (  11-)  C      N1     0.18    2.82  INTRA BL
 214 PHE   ( 448-)  A      O   <->  480 EDO   (  10-)  A      C1     0.18    2.62  INTRA BF
 453 DADE  (  11-)  B      N1  <->  464 DTHY  (   7-)  C      N3     0.17    2.83  INTRA BL
 271 LEU   ( 505-)  A      O   <->  286 ALA   ( 520-)  A      N      0.14    2.56  INTRA BL
 425 LYS   ( 659-)  A      C   <->  426 SER   ( 660-)  A      O      0.14    2.46  INTRA BF
And so on for a total of 58 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: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 437 MET   ( 946-)  D      -7.37
 147 LYS   ( 372-)  A      -6.24
 169 ARG   ( 399-)  A      -6.23
  35 TYR   ( 229-)  A      -6.20
 320 GLN   ( 554-)  A      -5.39
 397 ARG   ( 631-)  A      -5.36
 370 ARG   ( 604-)  A      -5.35
  43 CYS   ( 237-)  A      -5.21
  37 ASN   ( 231-)  A      -5.18

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: D

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.

 393 MET   ( 627-)  A   -2.95
 342 ALA   ( 576-)  A   -2.87
 143 LYS   ( 368-)  A   -2.73

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: D

Water, ion, and hydrogenbond related checks

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.

   2 GLN   ( 196-)  A
  27 HIS   ( 221-)  A
 136 GLN   ( 361-)  A
 166 ASN   ( 396-)  A
 269 ASN   ( 503-)  A
 295 GLN   ( 529-)  A
 396 ASN   ( 630-)  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.

   8 ARG   ( 202-)  A      NH2
  30 VAL   ( 224-)  A      N
  54 GLY   ( 248-)  A      N
  68 THR   ( 262-)  A      N
  73 THR   ( 284-)  A      N
  92 ASP   ( 303-)  A      N
  93 PHE   ( 304-)  A      N
 101 ALA   ( 326-)  A      N
 103 LYS   ( 328-)  A      N
 104 THR   ( 329-)  A      N
 153 TYR   ( 383-)  A      N
 173 VAL   ( 403-)  A      N
 185 PHE   ( 415-)  A      N
 212 ASP   ( 446-)  A      N
 227 VAL   ( 461-)  A      N
 238 ARG   ( 472-)  A      NE
 248 ASP   ( 482-)  A      N
 269 ASN   ( 503-)  A      N
 279 ASP   ( 513-)  A      N
 291 GLU   ( 525-)  A      N
 297 ASN   ( 531-)  A      N
 311 GLU   ( 545-)  A      N
 318 MET   ( 552-)  A      N
 341 GLU   ( 575-)  A      N
 344 ARG   ( 578-)  A      NE
 344 ARG   ( 578-)  A      NH2
 353 LYS   ( 587-)  A      N
 355 ASN   ( 589-)  A      N
 370 ARG   ( 604-)  A      NE
 395 THR   ( 629-)  A      N
 397 ARG   ( 631-)  A      N
 399 THR   ( 633-)  A      OG1
 428 ARG   ( 937-)  D      NE

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.

  92 ASP   ( 303-)  A      OD1
 295 GLN   ( 529-)  A      OE1
 341 GLU   ( 575-)  A      OE1
 376 HIS   ( 610-)  A      ND1

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.

 202 ASP   ( 432-)  A   H-bonding suggests Asn
 225 ASP   ( 459-)  A   H-bonding suggests Asn
 253 GLU   ( 487-)  A   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 :  -0.176
  2nd generation packing quality :  -1.726
  Ramachandran plot appearance   :  -1.047
  chi-1/chi-2 rotamer normality  :  -3.080 (poor)
  Backbone conformation          :  -0.438

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.881
  Bond angles                    :   1.101
  Omega angle restraints         :   1.195
  Side chain planarity           :   0.945
  Improper dihedral distribution :   0.955
  B-factor distribution          :   0.419
  Inside/Outside distribution    :   0.987

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 : 2.21


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.881
  Bond angles                    :   1.101
  Omega angle restraints         :   1.195
  Side chain planarity           :   0.945
  Improper dihedral distribution :   0.955
  B-factor distribution          :   0.419
  Inside/Outside distribution    :   0.987
==============

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

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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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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
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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.