WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1prh.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

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

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

Molecular weight of all polymer chains: 128712.039
Volume of the Unit Cell V= 4872975.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
but the number of MTRIX matrices flagged as `do not use` = 1
which seems more or less consistent with the SEQRES multiplicity
because the unitary MTRIX record gets forgotten more often ...
Matthews coefficient for observed atoms and Z high: Vm= 4.732
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.770

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.

1111 HEM   ( 601-)  A  -
1112 HEM   ( 601-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Rounded coordinates detected

At least two atoms were detected with all three coordinates rounded to 1 decimal place. Since this is highly unlikely to occur accidentally, the atoms listed in the table below were probably not refined. It could also be that ALL atomic coordinates were rounded to 1 or 2 decimal places (resulting in considerable loss of accuracy).

  98 TYR   ( 130-)  A      CE1    35.500    21.600   188.400
 240 LEU   ( 272-)  A      O    33.200    59.900   186.600
 379 THR   ( 411-)  A      O    24.300    65.700   196.600
 483 ASN   ( 515-)  A      CB    10.900    35.500   214.700
 501 GLY   ( 533-)  A      O    37.900    37.900   203.200
 599 TRP   (  77-)  B      O    68.600    26.900   221.500
 629 PHE   ( 107-)  B      CG    59.000     4.600   207.400
 648 SER   ( 126-)  B      C    52.600    34.100   203.500
 679 ARG   ( 157-)  B      CA    68.800    55.300   201.100

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.000

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: B

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.

  63 HIS   (  95-)  A      CB   CG    1.57    5.2
  63 HIS   (  95-)  A      CG   CD2   1.42    5.9
 107 TRP   ( 139-)  A      NE1  CE2   1.31   -5.4
 242 HIS   ( 274-)  A      CG   CD2   1.41    4.5
 291 TRP   ( 323-)  A      CG   CD2   1.35   -4.6
 291 TRP   ( 323-)  A      NE1  CE2   1.33   -4.0
 355 TRP   ( 387-)  A      NE1  CE2   1.32   -4.3
 356 HIS   ( 388-)  A      CG   CD2   1.40    4.1
 431 PHE   ( 463-)  A      N   -C     1.20   -6.2
 446 PHE   ( 478-)  A      N   -C     1.24   -4.3
 513 TRP   ( 545-)  A      CG   CD2   1.34   -4.9
 513 TRP   ( 545-)  A      NE1  CE2   1.32   -4.1
 617 HIS   (  95-)  B      CB   CG    1.58    5.6
 617 HIS   (  95-)  B      CG   CD2   1.42    5.4
 661 TRP   ( 139-)  B      NE1  CE2   1.31   -5.8
 796 HIS   ( 274-)  B      CG   CD2   1.40    4.3
 845 TRP   ( 323-)  B      CG   CD2   1.35   -4.4
 845 TRP   ( 323-)  B      NE1  CE2   1.32   -4.6
 909 TRP   ( 387-)  B      CG   CD2   1.36   -4.1
 909 TRP   ( 387-)  B      NE1  CE2   1.32   -4.3
 910 HIS   ( 388-)  B      CG   CD2   1.40    4.4
 985 PHE   ( 463-)  B      N   -C     1.20   -6.4
1000 PHE   ( 478-)  B      N   -C     1.24   -4.5
1067 TRP   ( 545-)  B      CG   CD2   1.34   -5.1
1067 TRP   ( 545-)  B      NE1  CE2   1.32   -4.2

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

 |  1.002705 -0.000219 -0.000050|
 | -0.000219  1.003545  0.000646|
 | -0.000050  0.000646  1.003379|
Proposed new scale matrix

 |  0.010033  0.000002  0.000000|
 |  0.000001  0.004738 -0.000003|
 |  0.000000 -0.000003  0.004276|
With corresponding cell

    A    =  99.672  B   = 211.050  C    = 233.888
    Alpha=  89.926  Beta=  90.002  Gamma=  90.025

The CRYST1 cell dimensions

    A    =  99.400  B   = 210.300  C    = 233.100
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 401.259
(Under-)estimated Z-score: 14.763

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.

   1 VAL   (  33-)  A      N    CA   C    98.22   -4.6
   2 ASN   (  34-)  A      N    CA   CB  119.30    5.2
   2 ASN   (  34-)  A      ND2  CG   OD1 116.53   -6.1
  10 GLN   (  42-)  A     -CA  -C    N   106.71   -4.7
  11 HIS   (  43-)  A      CA   CB   CG  109.18   -4.6
  11 HIS   (  43-)  A      CE1  NE2  CD2 112.32    4.2
  11 HIS   (  43-)  A      NE2  CD2  CG  100.42   -6.1
  11 HIS   (  43-)  A      CD2  CG   ND1 112.66    6.6
  11 HIS   (  43-)  A      CB   CG   CD2 123.78   -4.1
  18 PHE   (  50-)  A      CA   CB   CG  109.78   -4.0
  29 ARG   (  61-)  A      CA   CB   CG  122.89    4.4
  36 ASN   (  68-)  A      CA   CB   CG  117.94    5.3
  36 ASN   (  68-)  A      ND2  CG   OD1 117.40   -5.2
  43 TRP   (  75-)  A      CG   CD2  CE2 101.02   -5.2
  45 TRP   (  77-)  A      CB   CG   CD1 120.40   -4.3
  45 TRP   (  77-)  A      CD1  CG   CD2 113.16    4.3
  45 TRP   (  77-)  A      CG   CD1  NE1 104.78   -4.2
  45 TRP   (  77-)  A      CG   CD2  CE2 101.65   -4.6
  47 ARG   (  79-)  A      CB   CG   CD  105.19   -4.5
  47 ARG   (  79-)  A      CG   CD   NE  121.79    6.6
  47 ARG   (  79-)  A      CD   NE   CZ  130.67    5.0
  58 HIS   (  90-)  A      NE2  CD2  CG  101.76   -4.7
  58 HIS   (  90-)  A      CD2  CG   ND1 111.10    5.0
  58 HIS   (  90-)  A      CB   CG   CD2 123.60   -4.2
  59 PHE   (  91-)  A      CA   CB   CG  108.22   -5.6
And so on for a total of 440 lines.

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.

 105 ILE   ( 137-)  A      CB     6.3    40.54    32.31
 255 VAL   ( 287-)  A      CB    -6.7   -41.79   -32.96
 553 PRO   ( 585-)  A      N      7.5    22.24    -2.48
 659 ILE   ( 137-)  B      CB     6.0    40.13    32.31
 809 VAL   ( 287-)  B      CB    -6.7   -41.71   -32.96
1107 PRO   ( 585-)  B      N      7.5    22.22    -2.48
The average deviation= 1.531

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.

 741 GLY   ( 219-)  B    6.17
 187 GLY   ( 219-)  A    6.03
 669 TYR   ( 147-)  B    5.75
 115 TYR   ( 147-)  A    5.62
 742 PHE   ( 220-)  B    5.59
 197 ASP   ( 229-)  A    5.55
 228 GLU   ( 260-)  A    5.50
 188 PHE   ( 220-)  A    5.46
 751 ASP   ( 229-)  B    5.44
 782 GLU   ( 260-)  B    5.42
 239 VAL   ( 271-)  A    5.24
 793 VAL   ( 271-)  B    5.10
 338 GLN   ( 370-)  A    5.01
 892 GLN   ( 370-)  B    4.95
 809 VAL   ( 287-)  B    4.84
 255 VAL   ( 287-)  A    4.72
 545 TYR   ( 577-)  A    4.65
 488 GLU   ( 520-)  A    4.61
 555 VAL   (  33-)  B    4.61
1099 TYR   ( 577-)  B    4.57
   1 VAL   (  33-)  A    4.56
1042 GLU   ( 520-)  B    4.55
 528 LYS   ( 560-)  A    4.52
1082 LYS   ( 560-)  B    4.47
 123 VAL   ( 155-)  A    4.42
 677 VAL   ( 155-)  B    4.34
 293 ASP   ( 325-)  A    4.28
 118 ARG   ( 150-)  A    4.21
 847 ASP   ( 325-)  B    4.19
 666 ASN   ( 144-)  B    4.19
 114 SER   ( 146-)  A    4.17
 112 ASN   ( 144-)  A    4.16
 672 ARG   ( 150-)  B    4.14
 814 PHE   ( 292-)  B    4.12
 668 SER   ( 146-)  B    4.10
 552 ASP   ( 584-)  A    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.761

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.

1103 HIS   ( 581-)  B    4.61
 549 HIS   ( 581-)  A    4.24

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 565 HIS   (  43-)  B      CB   4.09
  11 HIS   (  43-)  A      CB   4.06
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.403

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.403

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.

 482 PRO   ( 514-)  A    -3.1
1036 PRO   ( 514-)  B    -3.1
 553 PRO   ( 585-)  A    -3.1
1107 PRO   ( 585-)  B    -3.1
1040 PHE   ( 518-)  B    -3.0
 486 PHE   ( 518-)  A    -3.0
 921 PRO   ( 399-)  B    -3.0
 367 PRO   ( 399-)  A    -3.0
  20 LEU   (  52-)  A    -2.8
 574 LEU   (  52-)  B    -2.8
  23 TYR   (  55-)  A    -2.8
 577 TYR   (  55-)  B    -2.8
 960 ARG   ( 438-)  B    -2.7
 406 ARG   ( 438-)  A    -2.7
 914 PRO   ( 392-)  B    -2.6
 360 PRO   ( 392-)  A    -2.6
 561 TYR   (  39-)  B    -2.5
 238 PRO   ( 270-)  A    -2.5
 115 TYR   ( 147-)  A    -2.5
 669 TYR   ( 147-)  B    -2.5
 792 PRO   ( 270-)  B    -2.5
 673 ILE   ( 151-)  B    -2.5
 119 ILE   ( 151-)  A    -2.5
   7 TYR   (  39-)  A    -2.4
1085 THR   ( 563-)  B    -2.4
And so on for a total of 77 lines.

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 ASN   (  34-)  A  Poor phi/psi
  19 GLY   (  51-)  A  Poor phi/psi
  20 LEU   (  52-)  A  Poor phi/psi
  34 GLY   (  66-)  A  PRO omega poor
  38 THR   (  70-)  A  Poor phi/psi
  94 SER   ( 126-)  A  PRO omega poor
  97 THR   ( 129-)  A  Poor phi/psi
 115 TYR   ( 147-)  A  Poor phi/psi
 116 TYR   ( 148-)  A  Poor phi/psi
 186 PRO   ( 218-)  A  omega poor
 188 PHE   ( 220-)  A  Poor phi/psi
 193 GLY   ( 225-)  A  omega poor
 196 VAL   ( 228-)  A  Poor phi/psi
 198 LEU   ( 230-)  A  Poor phi/psi
 215 PHE   ( 247-)  A  Poor phi/psi
 226 ASN   ( 258-)  A  Poor phi/psi
 227 GLY   ( 259-)  A  omega poor
 239 VAL   ( 271-)  A  Poor phi/psi
 240 LEU   ( 272-)  A  Poor phi/psi
 241 MET   ( 273-)  A  Poor phi/psi
 265 GLY   ( 297-)  A  Poor phi/psi
 290 THR   ( 322-)  A  omega poor
 354 HIS   ( 386-)  A  Poor phi/psi
 360 PRO   ( 392-)  A  Poor phi/psi
 377 PHE   ( 409-)  A  Poor phi/psi
And so on for a total of 64 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.954

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

  55 SER   (  87-)  A    0.36
 609 SER   (  87-)  B    0.36
 423 SER   ( 455-)  A    0.36
 977 SER   ( 455-)  B    0.36
 498 SER   ( 530-)  A    0.36
1052 SER   ( 530-)  B    0.36

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!

   4 CYS   (  36-)  A      0
   5 CYS   (  37-)  A      0
   7 TYR   (  39-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  11 HIS   (  43-)  A      0
  12 GLN   (  44-)  A      0
  18 PHE   (  50-)  A      0
  20 LEU   (  52-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 TYR   (  64-)  A      0
  33 SER   (  65-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  73 ALA   ( 105-)  A      0
  91 LEU   ( 123-)  A      0
  94 SER   ( 126-)  A      0
  95 PRO   ( 127-)  A      0
  96 PRO   ( 128-)  A      0
And so on for a total of 430 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!

 187 GLY   ( 219-)  A   2.99   26
 741 GLY   ( 219-)  B   2.98   27
 227 GLY   ( 259-)  A   1.58   63
 781 GLY   ( 259-)  B   1.57   68

Warning: Unusual peptide bond conformations

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

  11 HIS   (  43-)  A   1.53
 290 THR   ( 322-)  A   1.67
 355 TRP   ( 387-)  A   1.71
 844 THR   ( 322-)  B   1.71
 909 TRP   ( 387-)  B   1.67

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]

  93 PRO   ( 125-)  A    0.48 HIGH
  95 PRO   ( 127-)  A    0.45 HIGH
 186 PRO   ( 218-)  A    0.47 HIGH
 238 PRO   ( 270-)  A    0.49 HIGH
 264 PRO   ( 296-)  A    0.01 LOW
 430 PRO   ( 462-)  A    0.01 LOW
 482 PRO   ( 514-)  A    0.48 HIGH
 506 PRO   ( 538-)  A    0.49 HIGH
 647 PRO   ( 125-)  B    0.48 HIGH
 649 PRO   ( 127-)  B    0.45 HIGH
 675 PRO   ( 153-)  B    0.46 HIGH
 740 PRO   ( 218-)  B    0.46 HIGH
 792 PRO   ( 270-)  B    0.49 HIGH
 818 PRO   ( 296-)  B    0.00 LOW
 843 PRO   ( 321-)  B    0.45 HIGH
 984 PRO   ( 462-)  B    0.01 LOW
1036 PRO   ( 514-)  B    0.48 HIGH
1060 PRO   ( 538-)  B    0.49 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].

  54 PRO   (  86-)  A  -130.9 half-chair C-delta/C-gamma (-126 degrees)
  95 PRO   ( 127-)  A  -112.0 envelop C-gamma (-108 degrees)
 128 PRO   ( 160-)  A  -113.2 envelop C-gamma (-108 degrees)
 140 PRO   ( 172-)  A   109.2 envelop C-beta (108 degrees)
 159 PRO   ( 191-)  A  -113.3 envelop C-gamma (-108 degrees)
 238 PRO   ( 270-)  A   106.1 envelop C-beta (108 degrees)
 360 PRO   ( 392-)  A   -65.8 envelop C-beta (-72 degrees)
 482 PRO   ( 514-)  A   159.2 half-chair C-alpha/N (162 degrees)
 553 PRO   ( 585-)  A  -164.9 half-chair N/C-delta (-162 degrees)
 608 PRO   (  86-)  B  -131.1 half-chair C-delta/C-gamma (-126 degrees)
 649 PRO   ( 127-)  B  -112.2 envelop C-gamma (-108 degrees)
 682 PRO   ( 160-)  B  -112.6 envelop C-gamma (-108 degrees)
 694 PRO   ( 172-)  B   109.5 envelop C-beta (108 degrees)
 713 PRO   ( 191-)  B  -113.3 envelop C-gamma (-108 degrees)
 792 PRO   ( 270-)  B   106.1 envelop C-beta (108 degrees)
1036 PRO   ( 514-)  B   158.8 half-chair C-alpha/N (162 degrees)
1107 PRO   ( 585-)  B  -165.0 half-chair N/C-delta (-162 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.

 985 PHE   ( 463-)  B      CE2 <-> 1028 GLY   ( 506-)  B      C      0.50    2.70  INTRA BL
 431 PHE   ( 463-)  A      CE2 <->  474 GLY   ( 506-)  A      C      0.50    2.70  INTRA BL
 986 ASN   ( 464-)  B      ND2 <->  996 PRO   ( 474-)  B      CB     0.38    2.72  INTRA BL
 432 ASN   ( 464-)  A      ND2 <->  442 PRO   ( 474-)  A      CB     0.38    2.72  INTRA BL
1003 LEU   ( 481-)  B      CD1 <-> 1023 LEU   ( 501-)  B      CD2    0.33    2.87  INTRA BL
 449 LEU   ( 481-)  A      CD1 <->  469 LEU   ( 501-)  A      CD2    0.33    2.87  INTRA BL
 431 PHE   ( 463-)  A      CE2 <->  475 LEU   ( 507-)  A      N      0.31    2.79  INTRA BL
 985 PHE   ( 463-)  B      CE2 <-> 1029 LEU   ( 507-)  B      N      0.30    2.80  INTRA BL
 430 PRO   ( 462-)  A      CG  <->  433 GLU   ( 465-)  A      CG     0.24    2.96  INTRA BL
 984 PRO   ( 462-)  B      CG  <->  987 GLU   ( 465-)  B      CG     0.24    2.96  INTRA BL
 429 GLN   ( 461-)  A      CB  <->  430 PRO   ( 462-)  A      CD     0.21    2.89  INTRA BL
 432 ASN   ( 464-)  A      CG  <->  442 PRO   ( 474-)  A      CB     0.21    2.99  INTRA BL
 983 GLN   ( 461-)  B      CB  <->  984 PRO   ( 462-)  B      CD     0.21    2.89  INTRA BL
 986 ASN   ( 464-)  B      CG  <->  996 PRO   ( 474-)  B      CB     0.21    2.99  INTRA BL
 792 PRO   ( 270-)  B      O   <->  794 LEU   ( 272-)  B      N      0.21    2.49  INTRA BL
 264 PRO   ( 296-)  A      O   <->  268 LEU   ( 300-)  A      N      0.21    2.49  INTRA BL
 110 PHE   ( 142-)  A      O   <->  344 ARG   ( 376-)  A      NH2    0.21    2.49  INTRA BL
 664 PHE   ( 142-)  B      O   <->  898 ARG   ( 376-)  B      NH2    0.20    2.50  INTRA BL
 818 PRO   ( 296-)  B      O   <->  822 LEU   ( 300-)  B      N      0.20    2.50  INTRA BL
 238 PRO   ( 270-)  A      O   <->  240 LEU   ( 272-)  A      N      0.20    2.50  INTRA BL
 431 PHE   ( 463-)  A      CE2 <->  474 GLY   ( 506-)  A      CA     0.17    3.03  INTRA BL
 985 PHE   ( 463-)  B      CE2 <-> 1028 GLY   ( 506-)  B      CA     0.17    3.03  INTRA BL
 403 GLY   ( 435-)  A      C   <->  480 CYS   ( 512-)  A      SG     0.15    3.25  INTRA BL
 679 ARG   ( 157-)  B      CA  <->  981 ARG   ( 459-)  B      NH1    0.15    2.95  INTRA BL
 125 ARG   ( 157-)  A      CA  <->  427 ARG   ( 459-)  A      NH1    0.15    2.95  INTRA BL
And so on for a total of 115 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 799 ARG   ( 277-)  B      -7.06
 245 ARG   ( 277-)  A      -7.06
  29 ARG   (  61-)  A      -6.87
 583 ARG   (  61-)  B      -6.86
 692 GLN   ( 170-)  B      -6.47
 138 GLN   ( 170-)  A      -6.46
 240 LEU   ( 272-)  A      -6.13
 794 LEU   ( 272-)  B      -6.13
 896 ARG   ( 374-)  B      -6.08
 342 ARG   ( 374-)  A      -6.05
 137 LYS   ( 169-)  A      -6.05
 691 LYS   ( 169-)  B      -6.04
 707 ARG   ( 185-)  B      -5.90
 709 PHE   ( 187-)  B      -5.89
 155 PHE   ( 187-)  A      -5.89
 153 ARG   ( 185-)  A      -5.89
 737 LYS   ( 215-)  B      -5.87
 183 LYS   ( 215-)  A      -5.86
  51 ARG   (  83-)  A      -5.80
 679 ARG   ( 157-)  B      -5.76
 125 ARG   ( 157-)  A      -5.76
 605 ARG   (  83-)  B      -5.74
 702 ARG   ( 180-)  B      -5.52
 148 ARG   ( 180-)  A      -5.52
 955 ARG   ( 433-)  B      -5.42
 401 ARG   ( 433-)  A      -5.42
 541 LYS   ( 573-)  A      -5.31
1095 LYS   ( 573-)  B      -5.30
 950 ARG   ( 428-)  B      -5.27
 396 ARG   ( 428-)  A      -5.27
 965 HIS   ( 443-)  B      -5.11
 411 HIS   ( 443-)  A      -5.10
 918 ARG   ( 396-)  B      -5.07
 995 LYS   ( 473-)  B      -5.07
 364 ARG   ( 396-)  A      -5.07
 437 ARG   ( 469-)  A      -5.05
 991 ARG   ( 469-)  B      -5.05
 441 LYS   ( 473-)  A      -5.05
 242 HIS   ( 274-)  A      -5.00

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.

 137 LYS   ( 169-)  A       139 - LEU    171- ( A)         -5.70
 152 ARG   ( 184-)  A       155 - PHE    187- ( A)         -5.13
 245 ARG   ( 277-)  A       247 - ILE    279- ( A)         -5.12
 691 LYS   ( 169-)  B       693 - LEU    171- ( B)         -5.69
 706 ARG   ( 184-)  B       709 - PHE    187- ( B)         -5.13
 799 ARG   ( 277-)  B       801 - ILE    279- ( B)         -5.11

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

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

 966 ILE   ( 444-)  B   -2.60
 412 ILE   ( 444-)  A   -2.59

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.

 332 GLU   ( 364-)  A     -  335 PHE   ( 367-)  A        -1.87
 886 GLU   ( 364-)  B     -  889 PHE   ( 367-)  B        -1.87

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: 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.

 175 HIS   ( 207-)  A
 194 HIS   ( 226-)  A
 209 GLN   ( 241-)  A
 277 HIS   ( 309-)  A
 319 GLN   ( 351-)  A
 411 HIS   ( 443-)  A
 729 HIS   ( 207-)  B
 748 HIS   ( 226-)  B
 763 GLN   ( 241-)  B
 831 HIS   ( 309-)  B
 873 GLN   ( 351-)  B
 965 HIS   ( 443-)  B

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  20 LEU   (  52-)  A      N
  23 TYR   (  55-)  A      N
  36 ASN   (  68-)  A      N
  43 TRP   (  75-)  A      N
  65 ARG   (  97-)  A      NE
  99 ASN   ( 131-)  A      ND2
 100 ILE   ( 132-)  A      N
 106 SER   ( 138-)  A      OG
 115 TYR   ( 147-)  A      N
 116 TYR   ( 148-)  A      N
 117 THR   ( 149-)  A      N
 118 ARG   ( 150-)  A      NE
 118 ARG   ( 150-)  A      NH1
 118 ARG   ( 150-)  A      NH2
 138 GLN   ( 170-)  A      N
 153 ARG   ( 185-)  A      NE
 171 GLN   ( 203-)  A      NE2
 176 GLN   ( 208-)  A      NE2
 179 LYS   ( 211-)  A      NZ
 180 THR   ( 212-)  A      N
 181 SER   ( 213-)  A      OG
 182 GLY   ( 214-)  A      N
 189 THR   ( 221-)  A      N
 189 THR   ( 221-)  A      OG1
 191 ALA   ( 223-)  A      N
And so on for a total of 146 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

 176 GLN   ( 208-)  A      OE1
 288 HIS   ( 320-)  A      ND1
 307 GLU   ( 339-)  A      OE1
 369 ASP   ( 401-)  A      OD1
 539 ASN   ( 571-)  A      OD1
 730 GLN   ( 208-)  B      OE1
 754 HIS   ( 232-)  B      NE2
 842 HIS   ( 320-)  B      ND1
 861 GLU   ( 339-)  B      OE1
 923 ASP   ( 401-)  B      OD1
1093 ASN   ( 571-)  B      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  21 ASP   (  53-)  A   H-bonding suggests Asn
 197 ASP   ( 229-)  A   H-bonding suggests Asn; but Alt-Rotamer
 418 ASP   ( 450-)  A   H-bonding suggests Asn; Ligand-contact
 575 ASP   (  53-)  B   H-bonding suggests Asn
 751 ASP   ( 229-)  B   H-bonding suggests Asn; but Alt-Rotamer
 972 ASP   ( 450-)  B   H-bonding suggests Asn; Ligand-contact

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.053
  2nd generation packing quality :  -2.132
  Ramachandran plot appearance   :  -3.403 (poor)
  chi-1/chi-2 rotamer normality  :  -4.954 (bad)
  Backbone conformation          :  -1.348

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.883
  Bond angles                    :   1.632
  Omega angle restraints         :   0.968
  Side chain planarity           :   0.752
  Improper dihedral distribution :   1.312
  B-factor distribution          :   0.345
  Inside/Outside distribution    :   1.101

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 : 3.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -2.4
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.883
  Bond angles                    :   1.632
  Omega angle restraints         :   0.968
  Side chain planarity           :   0.752
  Improper dihedral distribution :   1.312
  B-factor distribution          :   0.345
  Inside/Outside distribution    :   1.101
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.