WHAT IF Check report

This file was created 2013-12-12 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 pdb4m6d.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  43.914  B   = 132.289  C    = 131.539
    Alpha= 118.590  Beta=  96.390  Gamma=  96.270

Dimensions of a reduced cell

    A    =  43.914  B   = 131.539  C    = 132.289
    Alpha= 118.590  Beta=  96.270  Gamma=  96.390

Dimensions of the conventional cell

    A    = 143.237  B   = 226.842  C    = 132.372
    Alpha=  90.394  Beta= 113.899  Gamma= 142.097

Transformation to conventional cell

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

Crystal class of the cell: TRICLINIC

Crystal class of the conventional CELL: TRIGONAL

Space group name: P 1

Bravais type of conventional cell is: R

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.919
CA-only RMS fit for the two chains : 0.460

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.788
CA-only RMS fit for the two chains : 0.430

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 0.838
CA-only RMS fit for the two chains : 0.433

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and G

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and I

All-atom RMS fit for the two chains : 0.680
CA-only RMS fit for the two chains : 0.325

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and I

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and K

All-atom RMS fit for the two chains : 0.799
CA-only RMS fit for the two chains : 0.349

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and K

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 743 ARG   (  61-)  I  -   CZ

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: C

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: K

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

Warning: B-factors outside the range 0.0 - 100.0

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

  13 LYS   (  13-)  A    High
  14 ARG   (  14-)  A    High
  15 HIS   (  15-)  A    High
  16 GLY   (  16-)  A    High
  17 LEU   (  17-)  A    High
  18 ASP   (  18-)  A    High
  19 ASN   (  19-)  A    High
  20 TYR   (  20-)  A    High
  21 ARG   (  21-)  A    High
  22 GLY   (  22-)  A    High
  23 TYR   (  23-)  A    High
  24 SER   (  24-)  A    High
  25 LEU   (  25-)  A    High
  26 GLY   (  26-)  A    High
  27 ASN   (  27-)  A    High
  28 TRP   (  28-)  A    High
  29 VAL   (  29-)  A    High
  30 CYS   (  30-)  A    High
  35 GLU   (  35-)  A    High
  44 ASN   (  44-)  A    High
  45 ARG   (  45-)  A    High
  46 ASN   (  46-)  A    High
  47 THR   (  47-)  A    High
  48 ASP   (  48-)  A    High
  49 GLY   (  49-)  A    High
And so on for a total of 662 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  86 SER   (  86-)  A    0.56
 256 SER   (  86-)  C    0.91
 427 SER   (  86-)  E    0.97
 597 SER   (  86-)  G    0.86
 768 SER   (  86-)  I    0.61
 938 SER   (  86-)  K    0.24

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: 12

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: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: K

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.

 128 ARG   ( 128-)  A
 231 ARG   (  61-)  C
 243 ARG   (  73-)  C
 298 ARG   ( 128-)  C
 469 ARG   ( 128-)  E
 572 ARG   (  61-)  G
 584 ARG   (  73-)  G
 639 ARG   ( 128-)  G
 743 ARG   (  61-)  I
 810 ARG   ( 128-)  I
 913 ARG   (  61-)  K
 925 ARG   (  73-)  K
 977 ARG   ( 125-)  K
 980 ARG   ( 128-)  K

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.

 119 ASP   ( 119-)  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.

  35 GLU   (  35-)  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.

 161 OCYT  (  41-)  B      N1   C6    1.39    4.4
 919 GLY   (  67-)  K      N    CA    1.52    4.3
 953 ASP   ( 101-)  K      CB   CG    1.63    4.6

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999057 -0.000223 -0.000088|
 | -0.000223  0.998398  0.000307|
 | -0.000088  0.000307  0.998925|
Proposed new scale matrix

 |  0.022794  0.002510  0.004376|
 |  0.000002  0.007616  0.004354|
 |  0.000000 -0.000003  0.008823|
With corresponding cell

    A    =  43.872  B   = 132.080  C    = 131.342
    Alpha= 118.543  Beta=  96.384  Gamma=  96.302

The CRYST1 cell dimensions

    A    =  43.914  B   = 132.289  C    = 131.539
    Alpha= 118.590  Beta=  96.390  Gamma=  96.270

Variance: 241.420
(Under-)estimated Z-score: 11.451

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.

  72 SER   (  72-)  A      CA   CB   OG  119.42    4.2
 108 TRP   ( 108-)  A      CA   CB   CG  104.59   -4.7
 130 OGUA  (  10-)  B      N9   C8   N7  113.11    4.0
 132 OGUA  (  12-)  B      N9   C8   N7  113.20    4.2
 133 OGUA  (  13-)  B      N9   C8   N7  113.13    4.1
 141 OGUA  (  21-)  B      N9   C8   N7  113.12    4.0
 143 OGUA  (  23-)  B      N9   C8   N7  113.13    4.1
 146 OGUA  (  26-)  B      N9   C8   N7  113.19    4.2
 148 OGUA  (  28-)  B      N9   C8   N7  113.17    4.1
 156 OGUA  (  36-)  B      N9   C8   N7  113.11    4.0
 163 OGUA  (  43-)  B      N9   C8   N7  113.14    4.1
 250 CYS   (  80-)  C      CA   CB   SG  105.13   -4.0
 300 OGUA  (   9-)  D      N9   C8   N7  113.11    4.0
 301 OGUA  (  10-)  D      N9   C8   N7  113.14    4.1
 303 OGUA  (  12-)  D      N9   C8   N7  113.14    4.1
 304 OGUA  (  13-)  D      N9   C8   N7  113.16    4.1
 310 OGUA  (  19-)  D      N9   C8   N7  113.14    4.1
 312 OGUA  (  21-)  D      N9   C8   N7  113.16    4.1
 314 OGUA  (  23-)  D      N9   C8   N7  113.11    4.0
 317 OGUA  (  26-)  D      N9   C8   N7  113.18    4.2
 319 OGUA  (  28-)  D      N9   C8   N7  113.16    4.1
 327 OGUA  (  36-)  D      N9   C8   N7  113.21    4.2
 334 OGUA  (  43-)  D      N9   C8   N7  113.13    4.1
 337 OGUA  (  46-)  D      N9   C8   N7  113.13    4.1
 340 OGUA  (  49-)  D      N9   C8   N7  113.10    4.0
And so on for a total of 68 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.

  35 GLU   (  35-)  A
 119 ASP   ( 119-)  A
 128 ARG   ( 128-)  A
 231 ARG   (  61-)  C
 243 ARG   (  73-)  C
 298 ARG   ( 128-)  C
 469 ARG   ( 128-)  E
 572 ARG   (  61-)  G
 584 ARG   (  73-)  G
 639 ARG   ( 128-)  G
 743 ARG   (  61-)  I
 810 ARG   ( 128-)  I
 913 ARG   (  61-)  K
 925 ARG   (  73-)  K
 977 ARG   ( 125-)  K
 980 ARG   ( 128-)  K

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.

 755 ARG   (  73-)  I    5.30
 947 ALA   (  95-)  K    4.17
 414 ARG   (  73-)  E    4.08
 260 ALA   (  90-)  C    4.06
 953 ASP   ( 101-)  K    4.06
 735 TYR   (  53-)  I    4.02

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 : -3.562

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.

 549 PHE   (  38-)  G    -3.1
 720 PHE   (  38-)  I    -2.8
  69 THR   (  69-)  A    -2.8
  78 ILE   (  78-)  A    -2.7
 760 ILE   (  78-)  I    -2.7
 890 PHE   (  38-)  K    -2.7
 930 ILE   (  78-)  K    -2.6
 737 ILE   (  55-)  I    -2.6
 620 VAL   ( 109-)  G    -2.5
 920 ARG   (  68-)  K    -2.5
 379 PHE   (  38-)  E    -2.4
 227 GLN   (  57-)  C    -2.4
 703 ARG   (  21-)  I    -2.4
 392 THR   (  51-)  E    -2.4
 976 ILE   ( 124-)  K    -2.4
 806 ILE   ( 124-)  I    -2.3
 208 PHE   (  38-)  C    -2.3
 921 THR   (  69-)  K    -2.3
 566 ILE   (  55-)  G    -2.3
  21 ARG   (  21-)  A    -2.3
 221 THR   (  51-)  C    -2.3
 751 THR   (  69-)  I    -2.2
 753 GLY   (  71-)  I    -2.2
 610 VAL   (  99-)  G    -2.2
 589 ILE   (  78-)  G    -2.2
 461 VAL   ( 120-)  E    -2.2
 954 GLY   ( 102-)  K    -2.2
 358 LEU   (  17-)  E    -2.2
  68 ARG   (  68-)  A    -2.2
 258 ILE   (  88-)  C    -2.1
 909 GLN   (  57-)  K    -2.1
 784 GLY   ( 102-)  I    -2.1
 455 ARG   ( 114-)  E    -2.1
 910 ILE   (  58-)  K    -2.1
 699 LEU   (  17-)  I    -2.1
 102 GLY   ( 102-)  A    -2.1
 899 THR   (  47-)  K    -2.1
 755 ARG   (  73-)  I    -2.1
 357 GLY   (  16-)  E    -2.1
 271 ASP   ( 101-)  C    -2.0
 272 GLY   ( 102-)  C    -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.

   3 PHE   (   3-)  A  omega poor
  16 GLY   (  16-)  A  Poor phi/psi
  19 ASN   (  19-)  A  omega poor
  21 ARG   (  21-)  A  Poor phi/psi
  37 ASN   (  37-)  A  Poor phi/psi
  38 PHE   (  38-)  A  Poor phi/psi
  53 TYR   (  53-)  A  omega poor
  57 GLN   (  57-)  A  Poor phi/psi
  62 TRP   (  62-)  A  omega poor
  70 PRO   (  70-)  A  omega poor
  74 ASN   (  74-)  A  Poor phi/psi
  77 ASN   (  77-)  A  Poor phi/psi
 100 SER   ( 100-)  A  Poor phi/psi, omega poor
 101 ASP   ( 101-)  A  Poor phi/psi, omega poor
 176 CYS   (   6-)  C  omega poor
 189 ASN   (  19-)  C  Poor phi/psi, omega poor
 191 ARG   (  21-)  C  Poor phi/psi
 207 ASN   (  37-)  C  Poor phi/psi
 208 PHE   (  38-)  C  Poor phi/psi
 223 TYR   (  53-)  C  omega poor
 232 TRP   (  62-)  C  omega poor
 237 GLY   (  67-)  C  Poor phi/psi
 238 ARG   (  68-)  C  omega poor
 243 ARG   (  73-)  C  Poor phi/psi
 244 ASN   (  74-)  C  Poor phi/psi
And so on for a total of 81 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 : -4.144

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.

 602 SER   (  91-)  G    0.36
 261 SER   (  91-)  C    0.39

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 PHE   (   3-)  A      0
  17 LEU   (  17-)  A      0
  18 ASP   (  18-)  A      0
  19 ASN   (  19-)  A      0
  20 TYR   (  20-)  A      0
  21 ARG   (  21-)  A      0
  36 SER   (  36-)  A      0
  37 ASN   (  37-)  A      0
  38 PHE   (  38-)  A      0
  39 ASN   (  39-)  A      0
  42 ALA   (  42-)  A      0
  50 SER   (  50-)  A      0
  53 TYR   (  53-)  A      0
  56 LEU   (  56-)  A      0
  57 GLN   (  57-)  A      0
  59 ASN   (  59-)  A      0
  61 ARG   (  61-)  A      0
  62 TRP   (  62-)  A      0
  63 TRP   (  63-)  A      0
  66 ASP   (  66-)  A      0
  68 ARG   (  68-)  A      0
  73 ARG   (  73-)  A      0
  76 CYS   (  76-)  A      0
  77 ASN   (  77-)  A      0
  89 THR   (  89-)  A      0
And so on for a total of 596 lines.

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 7.533

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!

 784 GLY   ( 102-)  I   1.81   17
 102 GLY   ( 102-)  A   1.55   15
 753 GLY   (  71-)  I   1.51   80

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].

 581 PRO   (  70-)  G    49.6 half-chair C-delta/C-gamma (54 degrees)
 590 PRO   (  79-)  G  -124.8 half-chair C-delta/C-gamma (-126 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.

 987 OCYT  (  14-)  L      N3  <->  988 OURA  (  15-)  L      C5     0.65    2.45  INTRA BF
 999 OGUA  (  26-)  L      N2  <-> 1015 OURA  (  42-)  L      C2     0.57    2.53  INTRA BF
 541 CYS   (  30-)  G      SG  <->  634 TRP   ( 123-)  G      NE1    0.56    2.74  INTRA BF
 987 OCYT  (  14-)  L      C2  <->  988 OURA  (  15-)  L      C5     0.54    2.66  INTRA BF
 814 OGUA  (  12-)  J      O6  <->  850 OCYT  (  48-)  J      N3     0.51    2.04  INTRA BF
1001 OGUA  (  28-)  L      N2  <-> 1013 OADE  (  40-)  L      N7     0.50    2.50  INTRA BF
 662 OURA  (  30-)  H      N3  <->  667 OADE  (  35-)  H      N1     0.48    2.52  INTRA BL
 728 ASN   (  46-)  I      ND2 <->  734 ASP   (  52-)  I      OD1    0.46    2.24  INTRA BL
 983 OGUA  (  10-)  L      C2  <-> 1024 OCYT  (  51-)  L      N4     0.44    2.66  INTRA BF
 132 OGUA  (  12-)  B      O6  <->  168 OCYT  (  48-)  B      N4     0.44    2.26  INTRA BF
 136 OADE  (  16-)  B      C8  <->  137 OADE  (  17-)  B      N6     0.41    2.69  INTRA BL
 224 GLY   (  54-)  C      O   <->  227 GLN   (  57-)  C      NE2    0.40    2.30  INTRA BL
 371 CYS   (  30-)  E      CB  <->  464 TRP   ( 123-)  E      CE2    0.39    2.81  INTRA BL
 727 ARG   (  45-)  I      NH1 <->  733 THR   (  51-)  I      OG1    0.38    2.32  INTRA BL
 914 TRP   (  62-)  K      O   <->  927 LEU   (  75-)  K      N      0.38    2.32  INTRA BL
 987 OCYT  (  14-)  L      C4  <->  988 OURA  (  15-)  L      C5     0.38    2.82  INTRA BF
 997 OCYT  (  24-)  L      N3  <-> 1016 OGUA  (  43-)  L      N1     0.37    2.63  INTRA BF
 300 OGUA  (   9-)  D      N2  <->  301 OGUA  (  10-)  D      C6     0.37    2.73  INTRA BF
 147 OADE  (  27-)  B      C2  <->  161 OCYT  (  41-)  B      N3     0.37    2.73  INTRA BF
 818 OADE  (  16-)  J      O2' <->  820 OADE  (  18-)  J      N6     0.36    2.34  INTRA BF
 660 OGUA  (  28-)  H      N2  <->  672 OADE  (  40-)  H      N7     0.35    2.65  INTRA BF
 818 OADE  (  16-)  J      C8  <->  819 OADE  (  17-)  J      N6     0.35    2.75  INTRA BF
 657 OADE  (  25-)  H      N6  <->  674 OURA  (  42-)  H      O4     0.33    2.37  INTRA BL
 897 ARG   (  45-)  K      NE  <->  903 THR   (  51-)  K      OG1    0.33    2.37  INTRA BL
 306 OURA  (  15-)  D      N3  <->  336 OADE  (  45-)  D      N1     0.33    2.67  INTRA BF
And so on for a total of 359 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

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.

 639 ARG   ( 128-)  G      -8.43
 128 ARG   ( 128-)  A      -8.37
 298 ARG   ( 128-)  C      -8.30
 469 ARG   ( 128-)  E      -8.30
 980 ARG   ( 128-)  K      -8.27
 810 ARG   ( 128-)  I      -7.95
 750 ARG   (  68-)  I      -7.31
 920 ARG   (  68-)  K      -7.23
  68 ARG   (  68-)  A      -7.18
 579 ARG   (  68-)  G      -7.12
 409 ARG   (  68-)  E      -6.78
 238 ARG   (  68-)  C      -6.28
 977 ARG   ( 125-)  K      -6.25
 191 ARG   (  21-)  C      -6.01
  14 ARG   (  14-)  A      -5.88
 867 HIS   (  15-)  K      -5.84
 873 ARG   (  21-)  K      -5.73
 525 ARG   (  14-)  G      -5.73
 532 ARG   (  21-)  G      -5.70
 355 ARG   (  14-)  E      -5.70
 866 ARG   (  14-)  K      -5.69
 184 ARG   (  14-)  C      -5.67
 466 ARG   ( 125-)  E      -5.66
 295 ARG   ( 125-)  C      -5.65
 696 ARG   (  14-)  I      -5.65
  21 ARG   (  21-)  A      -5.65
 703 ARG   (  21-)  I      -5.51
 362 ARG   (  21-)  E      -5.50
 584 ARG   (  73-)  G      -5.44
 965 ASN   ( 113-)  K      -5.33
 113 ASN   ( 113-)  A      -5.32
 125 ARG   ( 125-)  A      -5.20
 795 ASN   ( 113-)  I      -5.15
 556 ARG   (  45-)  G      -5.10
 636 ARG   ( 125-)  G      -5.09
 807 ARG   ( 125-)  I      -5.02

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.

 453 ARG   ( 112-)  E       455 - ARG    114- ( E)         -4.61

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

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

Average for range 1 - 1024 : -1.514

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: C

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: E

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: G

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: I

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: K

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.

 298 ARG   ( 128-)  C   -2.88
 128 ARG   ( 128-)  A   -2.86
 639 ARG   ( 128-)  G   -2.85
 980 ARG   ( 128-)  K   -2.83
 469 ARG   ( 128-)  E   -2.82
 810 ARG   ( 128-)  I   -2.73
 957 MET   ( 105-)  K   -2.66
 936 LEU   (  84-)  K   -2.64
 766 LEU   (  84-)  I   -2.64
 425 LEU   (  84-)  E   -2.61
 446 MET   ( 105-)  E   -2.53

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: C

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: K

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1039 HOH   ( 207 )  I      O    -11.47  -52.11  -59.71

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.

1033 HOH   ( 205 )  C      O
1036 HOH   ( 109 )  F      O

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.

  46 ASN   (  46-)  A
  65 ASN   (  65-)  A
 229 ASN   (  59-)  C
 454 ASN   ( 113-)  E
 462 GLN   ( 121-)  E
 726 ASN   (  44-)  I
 879 ASN   (  27-)  K
 909 GLN   (  57-)  K
 926 ASN   (  74-)  K
 965 ASN   ( 113-)  K
 973 GLN   ( 121-)  K

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.

   5 ARG   (   5-)  A      NH1
  18 ASP   (  18-)  A      N
  20 TYR   (  20-)  A      N
  28 TRP   (  28-)  A      NE1
  45 ARG   (  45-)  A      NH1
  51 THR   (  51-)  A      OG1
  55 ILE   (  55-)  A      N
  56 LEU   (  56-)  A      N
  57 GLN   (  57-)  A      NE2
  64 CYS   (  64-)  A      N
  68 ARG   (  68-)  A      NE
  73 ARG   (  73-)  A      NH1
  74 ASN   (  74-)  A      N
  91 SER   (  91-)  A      OG
 102 GLY   ( 102-)  A      N
 106 ASN   ( 106-)  A      N
 107 ALA   ( 107-)  A      N
 109 VAL   ( 109-)  A      N
 111 TRP   ( 111-)  A      N
 123 TRP   ( 123-)  A      N
 128 ARG   ( 128-)  A      NH2
 158 OURA  (  38-)  B      N3
 188 ASP   (  18-)  C      N
 196 GLY   (  26-)  C      N
 225 ILE   (  55-)  C      N
And so on for a total of 123 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.

 271 ASP   ( 101-)  C      OD2
 697 HIS   (  15-)  I      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.

  35 GLU   (  35-)  A   H-bonding suggests Gln
 101 ASP   ( 101-)  A   H-bonding suggests Asn
 222 ASP   (  52-)  C   H-bonding suggests Asn
 271 ASP   ( 101-)  C   H-bonding suggests Asn
 393 ASP   (  52-)  E   H-bonding suggests Asn; but Alt-Rotamer
 783 ASP   ( 101-)  I   H-bonding suggests Asn
 904 ASP   (  52-)  K   H-bonding suggests Asn

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 :  -2.536
  2nd generation packing quality :  -1.677
  Ramachandran plot appearance   :  -3.562 (poor)
  chi-1/chi-2 rotamer normality  :  -4.144 (bad)
  Backbone conformation          :  -0.906

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.667
  Bond angles                    :   0.775
  Omega angle restraints         :   1.370 (loose)
  Side chain planarity           :   0.546 (tight)
  Improper dihedral distribution :   0.819
  B-factor distribution          :   1.334
  Inside/Outside distribution    :   0.941

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 : 2.68


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.8
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.667
  Bond angles                    :   0.775
  Omega angle restraints         :   1.370 (loose)
  Side chain planarity           :   0.546 (tight)
  Improper dihedral distribution :   0.819
  B-factor distribution          :   1.334
  Inside/Outside distribution    :   0.941
==============

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.