WHAT IF Check report

This file was created 2012-01-04 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 pdb1kxv.ent

Checks that need to be done early-on in validation

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 B

All-atom RMS fit for the two chains : 0.587
CA-only RMS fit for the two chains : 0.468

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 B

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: C and D

All-atom RMS fit for the two chains : 0.843
CA-only RMS fit for the two chains : 0.453

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: C and D

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 484 GLU   ( 484-)  A  -
 979 GLU   ( 484-)  B  -
1117 GLY   (   8-)  D  -

Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 243 LYS   ( 243-)  A      CG
 243 LYS   ( 243-)  A      CD
 243 LYS   ( 243-)  A      CE
 243 LYS   ( 243-)  A      NZ
 343 ARG   ( 343-)  A      CG
 343 ARG   ( 343-)  A      CD
 343 ARG   ( 343-)  A      NE
 343 ARG   ( 343-)  A      CZ
 343 ARG   ( 343-)  A      NH1
 343 ARG   ( 343-)  A      NH2
 838 ARG   ( 343-)  B      CG
 838 ARG   ( 343-)  B      CD
 838 ARG   ( 343-)  B      NE
 838 ARG   ( 343-)  B      CZ
 838 ARG   ( 343-)  B      NH1
 838 ARG   ( 343-)  B      NH2
 960 ILE   ( 465-)  B      CG1
 960 ILE   ( 465-)  B      CG2
 960 ILE   ( 465-)  B      CD1
 963 TYR   ( 468-)  B      CG
 963 TYR   ( 468-)  B      CD1
 963 TYR   ( 468-)  B      CD2
 963 TYR   ( 468-)  B      CE1
 963 TYR   ( 468-)  B      CE2
 963 TYR   ( 468-)  B      CZ
 963 TYR   ( 468-)  B      OH

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:

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: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Valine nomenclature problem

The valine residues listed in the table below have their C-gamma-1 and C-gamma-2 swapped.

1168 VAL   (  60-)  D

Warning: Arginine nomenclature problem

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

  10 ARG   (  10-)  A
  20 ARG   (  20-)  A
  30 ARG   (  30-)  A
  56 ARG   (  56-)  A
  61 ARG   (  61-)  A
  72 ARG   (  72-)  A
  80 ARG   (  80-)  A
  85 ARG   (  85-)  A
  92 ARG   (  92-)  A
 124 ARG   ( 124-)  A
 158 ARG   ( 158-)  A
 176 ARG   ( 176-)  A
 195 ARG   ( 195-)  A
 252 ARG   ( 252-)  A
 267 ARG   ( 267-)  A
 291 ARG   ( 291-)  A
 303 ARG   ( 303-)  A
 319 ARG   ( 319-)  A
 337 ARG   ( 337-)  A
 346 ARG   ( 346-)  A
 387 ARG   ( 387-)  A
 389 ARG   ( 389-)  A
 392 ARG   ( 392-)  A
 398 ARG   ( 398-)  A
 421 ARG   ( 421-)  A
And so on for a total of 54 lines.

Warning: Tyrosine convention problem

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

  31 TYR   (  31-)  A
  62 TYR   (  62-)  A
 151 TYR   ( 151-)  A
 182 TYR   ( 182-)  A
 247 TYR   ( 247-)  A
 276 TYR   ( 276-)  A
 449 TYR   ( 449-)  A
 526 TYR   (  31-)  B
 589 TYR   (  94-)  B
 646 TYR   ( 151-)  B
 677 TYR   ( 182-)  B
 742 TYR   ( 247-)  B
 771 TYR   ( 276-)  B
 828 TYR   ( 333-)  B
 944 TYR   ( 449-)  B
1021 TYR   (  32-)  C
1083 TYR   (  94-)  C
1090 TYR   ( 101-)  C
1140 TYR   (  32-)  D
1187 TYR   (  79-)  D
1202 TYR   (  94-)  D
1209 TYR   ( 101-)  D

Warning: Phenylalanine convention problem

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

  17 PHE   (  17-)  A
 194 PHE   ( 194-)  A
 229 PHE   ( 229-)  A
 231 PHE   ( 231-)  A
 256 PHE   ( 256-)  A
 286 PHE   ( 286-)  A
 295 PHE   ( 295-)  A
 315 PHE   ( 315-)  A
 327 PHE   ( 327-)  A
 397 PHE   ( 397-)  A
 406 PHE   ( 406-)  A
 419 PHE   ( 419-)  A
 486 PHE   ( 487-)  A
 512 PHE   (  17-)  B
 689 PHE   ( 194-)  B
 717 PHE   ( 222-)  B
 724 PHE   ( 229-)  B
 726 PHE   ( 231-)  B
 751 PHE   ( 256-)  B
 781 PHE   ( 286-)  B
 790 PHE   ( 295-)  B
 822 PHE   ( 327-)  B
 892 PHE   ( 397-)  B
 901 PHE   ( 406-)  B
 981 PHE   ( 487-)  B
1036 PHE   (  47-)  C

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.

  23 ASP   (  23-)  A
  96 ASP   (  96-)  A
 135 ASP   ( 135-)  A
 138 ASP   ( 138-)  A
 153 ASP   ( 153-)  A
 159 ASP   ( 159-)  A
 167 ASP   ( 167-)  A
 181 ASP   ( 181-)  A
 188 ASP   ( 188-)  A
 197 ASP   ( 197-)  A
 206 ASP   ( 206-)  A
 353 ASP   ( 353-)  A
 375 ASP   ( 375-)  A
 402 ASP   ( 402-)  A
 432 ASP   ( 432-)  A
 433 ASP   ( 433-)  A
 451 ASP   ( 451-)  A
 456 ASP   ( 456-)  A
 472 ASP   ( 472-)  A
 518 ASP   (  23-)  B
 591 ASP   (  96-)  B
 630 ASP   ( 135-)  B
 633 ASP   ( 138-)  B
 648 ASP   ( 153-)  B
 654 ASP   ( 159-)  B
 676 ASP   ( 181-)  B
 683 ASP   ( 188-)  B
 692 ASP   ( 197-)  B
 701 ASP   ( 206-)  B
 848 ASP   ( 353-)  B
 870 ASP   ( 375-)  B
 897 ASP   ( 402-)  B
 927 ASP   ( 432-)  B
 928 ASP   ( 433-)  B
 946 ASP   ( 451-)  B
 951 ASP   ( 456-)  B
 967 ASP   ( 472-)  B
1041 ASP   (  52-)  C
1043 ASP   (  54-)  C
1141 ASP   (  33-)  D
1160 ASP   (  52-)  D
1162 ASP   (  54-)  D

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.

  47 GLU   (  47-)  A
  60 GLU   (  60-)  A
  76 GLU   (  76-)  A
 125 GLU   ( 125-)  A
 149 GLU   ( 149-)  A
 171 GLU   ( 171-)  A
 233 GLU   ( 233-)  A
 240 GLU   ( 240-)  A
 246 GLU   ( 246-)  A
 272 GLU   ( 272-)  A
 282 GLU   ( 282-)  A
 352 GLU   ( 352-)  A
 385 GLU   ( 385-)  A
 390 GLU   ( 390-)  A
 484 GLU   ( 484-)  A
 492 GLU   ( 493-)  A
 542 GLU   (  47-)  B
 555 GLU   (  60-)  B
 571 GLU   (  76-)  B
 620 GLU   ( 125-)  B
 644 GLU   ( 149-)  B
 666 GLU   ( 171-)  B
 728 GLU   ( 233-)  B
 735 GLU   ( 240-)  B
 741 GLU   ( 246-)  B
 767 GLU   ( 272-)  B
 847 GLU   ( 352-)  B
 880 GLU   ( 385-)  B
 885 GLU   ( 390-)  B
 979 GLU   ( 484-)  B
 987 GLU   ( 493-)  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.

 252 ARG   ( 252-)  A      CG   CD    1.65    4.3
 253 VAL   ( 253-)  A      CA   CB    1.63    4.8
 395 VAL   ( 395-)  A      CA   CB    1.62    4.6
 785 ASP   ( 290-)  B      CG   OD2   1.34    4.7
 916 ARG   ( 421-)  B      CD   NE    1.36   -5.4
 916 ARG   ( 421-)  B      NE   CZ    1.27   -4.1
1111 VAL   (   2-)  D      N   -C     1.18   -7.4
1117 GLY   (   8-)  D      C    O     1.15   -4.0
1120 VAL   (  12-)  D      CA   CB    1.45   -4.1
1144 TRP   (  36-)  D      NE1  CE2   1.32   -4.6
1185 THR   (  77-)  D      CA   CB    1.42   -5.4
1223 THR   ( 115-)  D      CB   OG1   1.37   -4.2
1229 SER   ( 121-)  D      N    CA    1.57    6.0
1229 SER   ( 121-)  D      N   -C     1.44    5.7

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

 |  0.995490 -0.000459 -0.001194|
 | -0.000459  0.995487  0.000170|
 | -0.001194  0.000170  0.996338|
Proposed new scale matrix

 |  0.017456  0.003444  0.004125|
 |  0.000012  0.016786  0.003354|
 |  0.000012 -0.000002  0.009712|
With corresponding cell

    A    =  57.308  B   =  60.726  C    = 106.965
    Alpha=  98.716  Beta= 100.992  Gamma= 101.192

The CRYST1 cell dimensions

    A    =  57.568  B   =  60.990  C    = 107.333
    Alpha=  98.780  Beta= 100.880  Gamma= 101.140

Variance: 752.360
(Under-)estimated Z-score: 20.215

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.

  10 ARG   (  10-)  A      CB   CG   CD  122.67    4.3
  10 ARG   (  10-)  A      CD   NE   CZ  131.72    5.6
  10 ARG   (  10-)  A      NE   CZ   NH1 128.14    4.3
  10 ARG   (  10-)  A      NE   CZ   NH2 111.91   -4.3
  70 CYS   (  70-)  A      N    CA   CB  101.43   -5.3
  72 ARG   (  72-)  A      CB   CG   CD  102.72   -5.7
  72 ARG   (  72-)  A      CD   NE   CZ  133.03    6.3
  72 ARG   (  72-)  A      NE   CZ   NH1 128.40    4.4
  72 ARG   (  72-)  A      NE   CZ   NH2 111.95   -4.2
  92 ARG   (  92-)  A      CB   CG   CD  130.26    8.1
  92 ARG   (  92-)  A      CD   NE   CZ  133.45    6.5
  92 ARG   (  92-)  A      NE   CZ   NH1 127.62    4.0
 101 HIS   ( 101-)  A      CG   ND1  CE1 109.63    4.0
 176 ARG   ( 176-)  A      CB   CG   CD  132.63    9.3
 176 ARG   ( 176-)  A      CD   NE   CZ  131.64    5.5
 176 ARG   ( 176-)  A      NE   CZ   NH1 128.40    4.4
 176 ARG   ( 176-)  A      NE   CZ   NH2 111.77   -4.3
 195 ARG   ( 195-)  A      CG   CD   NE  101.80   -5.1
 195 ARG   ( 195-)  A      CD   NE   CZ  134.00    6.8
 195 ARG   ( 195-)  A      NE   CZ   NH1 130.61    5.6
 195 ARG   ( 195-)  A      NE   CZ   NH2 109.79   -5.4
 201 HIS   ( 201-)  A      CG   ND1  CE1 109.62    4.0
 225 GLY   ( 225-)  A     -O   -C    N   114.55   -5.3
 225 GLY   ( 225-)  A     -C    N    CA  104.09   -9.7
 252 ARG   ( 252-)  A      CB   CG   CD  132.04    9.0
And so on for a total of 87 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.

  10 ARG   (  10-)  A
  20 ARG   (  20-)  A
  23 ASP   (  23-)  A
  30 ARG   (  30-)  A
  47 GLU   (  47-)  A
  56 ARG   (  56-)  A
  60 GLU   (  60-)  A
  61 ARG   (  61-)  A
  72 ARG   (  72-)  A
  76 GLU   (  76-)  A
  80 ARG   (  80-)  A
  85 ARG   (  85-)  A
  92 ARG   (  92-)  A
  96 ASP   (  96-)  A
 124 ARG   ( 124-)  A
 125 GLU   ( 125-)  A
 135 ASP   ( 135-)  A
 138 ASP   ( 138-)  A
 149 GLU   ( 149-)  A
 153 ASP   ( 153-)  A
 158 ARG   ( 158-)  A
 159 ASP   ( 159-)  A
 167 ASP   ( 167-)  A
 171 GLU   ( 171-)  A
 176 ARG   ( 176-)  A
And so on for a total of 128 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.

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

 395 VAL   ( 395-)  A      CB     9.0   -21.16   -32.96
1120 VAL   (  12-)  D      CB     7.2   -23.52   -32.96
1168 VAL   (  60-)  D      CB    25.4     0.26   -32.96 Wrong hand
1229 SER   ( 121-)  D      CA    -8.3    18.83    34.32
The average deviation= 1.222

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.

1229 SER   ( 121-)  D    6.77
1132 ALA   (  24-)  D    6.38
 133 ALA   ( 133-)  A    5.37
 657 LEU   ( 162-)  B    5.18
 318 ALA   ( 318-)  A    4.89
 292 ALA   ( 292-)  A    4.68
1117 GLY   (   8-)  D    4.65
 293 LEU   ( 293-)  A    4.51
 813 ALA   ( 318-)  B    4.46
 788 LEU   ( 293-)  B    4.36
 799 GLY   ( 304-)  B    4.28
 831 THR   ( 336-)  B    4.18
 317 ASP   ( 317-)  A    4.16
 336 THR   ( 336-)  A    4.15
 787 ALA   ( 292-)  B    4.14

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 871 THR   ( 376-)  B    -2.6
  45 PRO   (  45-)  A    -2.6
 658 VAL   ( 163-)  B    -2.5
 376 THR   ( 376-)  A    -2.5
1126 LEU   (  18-)  D    -2.3
1218 PRO   ( 110-)  D    -2.3
 540 PRO   (  45-)  B    -2.2
 270 SER   ( 270-)  A    -2.2
  49 ILE   (  49-)  A    -2.2
  69 LEU   (  69-)  A    -2.2
 163 VAL   ( 163-)  A    -2.2
1120 VAL   (  12-)  D    -2.2
 587 ARG   (  92-)  B    -2.1
1200 MET   (  92-)  D    -2.0
 561 SER   (  66-)  B    -2.0
  92 ARG   (  92-)  A    -2.0
1149 PRO   (  41-)  D    -2.0
 551 ARG   (  56-)  B    -2.0
 947 VAL   ( 452-)  B    -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.

   5 GLN   (   5-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
 102 MET   ( 102-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 225 GLY   ( 225-)  A  omega poor
 268 LYS   ( 268-)  A  Poor phi/psi
 376 THR   ( 376-)  A  Poor phi/psi
 380 ASN   ( 380-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 384 CYS   ( 384-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 500 GLN   (   5-)  B  Poor phi/psi
 513 GLU   (  18-)  B  Poor phi/psi
 548 ASN   (  53-)  B  PRO omega poor
 597 MET   ( 102-)  B  Poor phi/psi
 619 ARG   ( 124-)  B  Poor phi/psi
 624 VAL   ( 129-)  B  PRO omega poor
 719 ALA   ( 224-)  B  Poor phi/psi
 720 GLY   ( 225-)  B  Poor phi/psi
 763 LYS   ( 268-)  B  Poor phi/psi
 845 ASN   ( 350-)  B  Poor phi/psi
 859 ASN   ( 364-)  B  Poor phi/psi
 871 THR   ( 376-)  B  Poor phi/psi
 875 ASN   ( 380-)  B  Poor phi/psi
 876 ASP   ( 381-)  B  Poor phi/psi
 909 SER   ( 414-)  B  Poor phi/psi
1065 ASN   (  76-)  C  Poor phi/psi
1080 ALA   (  91-)  C  Poor phi/psi
1184 ASN   (  76-)  D  Poor phi/psi
1199 ALA   (  91-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.047

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!

   5 GLN   (   5-)  A      0
   8 SER   (   8-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  21 TRP   (  21-)  A      0
  30 ARG   (  30-)  A      0
  31 TYR   (  31-)  A      0
  32 LEU   (  32-)  A      0
  37 PHE   (  37-)  A      0
  45 PRO   (  45-)  A      0
  48 ASN   (  48-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 SER   (  55-)  A      0
  56 ARG   (  56-)  A      0
  58 TRP   (  58-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
And so on for a total of 539 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 3.236

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]

 121 PRO   ( 121-)  A    0.45 HIGH
 405 PRO   ( 405-)  A    0.46 HIGH
1002 PRO   (  13-)  C    0.02 LOW
1030 PRO   (  41-)  C    0.47 HIGH
1086 PRO   (  97-)  C    0.02 LOW
1093 PRO   ( 104-)  C    0.45 HIGH
1121 PRO   (  13-)  D    0.03 LOW
1149 PRO   (  41-)  D    0.45 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].

 228 PRO   ( 228-)  A  -119.2 half-chair C-delta/C-gamma (-126 degrees)
 718 PRO   ( 223-)  B  -122.9 half-chair C-delta/C-gamma (-126 degrees)
 855 PRO   ( 360-)  B  -112.9 envelop C-gamma (-108 degrees)
1076 PRO   (  87-)  C  -126.4 half-chair C-delta/C-gamma (-126 degrees)
1212 PRO   ( 104-)  D  -113.2 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

 777 GLU   ( 282-)  B      OE1 <-> 1234 HOH   ( 626 )  B      O      0.74    1.66  INTRA
   1 GLN   (   1-)  A      N   <->  228 PRO   ( 228-)  A      O      0.67    2.03  INTRA
 665 LEU   ( 170-)  B      O   <->  671 ARG   ( 176-)  B      CD     0.65    2.15  INTRA
1229 SER   ( 121-)  D      O   <-> 1232 SER   ( 121-)  D      O''    0.63    0.87  INTRA B2
 170 LEU   ( 170-)  A      O   <->  176 ARG   ( 176-)  A      CD     0.61    2.19  INTRA
 850 ASN   ( 355-)  B      ND2 <-> 1234 HOH   ( 805 )  B      O      0.55    2.15  INTRA
1169 ASP   (  61-)  D      OD2 <-> 1236 HOH   ( 159 )  D      O      0.53    1.87  INTRA BF
 761 VAL   ( 266-)  B      CG1 <->  818 ILE   ( 323-)  B      CD1    0.53    2.67  INTRA
  72 ARG   (  72-)  A      CD  <-> 1233 HOH   ( 545 )  A      O      0.52    2.28  INTRA
 904 TRP   ( 409-)  B      CH2 <->  912 VAL   ( 417-)  B      CG1    0.49    2.71  INTRA
 544 ILE   (  49-)  B      CG2 <->  598 CYS   ( 103-)  B      CB     0.48    2.72  INTRA
 409 TRP   ( 409-)  A      CH2 <->  417 VAL   ( 417-)  A      CG1    0.45    2.75  INTRA BL
 207 ILE   ( 207-)  A      O   <->  211 LEU   ( 211-)  A      CD1    0.44    2.36  INTRA
 841 ARG   ( 346-)  B      C   <-> 1234 HOH   ( 805 )  B      O      0.43    2.37  INTRA BF
 421 ARG   ( 421-)  A      NH2 <-> 1233 HOH   ( 723 )  A      O      0.43    2.27  INTRA
   5 GLN   (   5-)  A      O   <->   92 ARG   (  92-)  A      CD     0.42    2.38  INTRA
 496 GLN   (   1-)  B      NE2 <-> 1234 HOH   ( 799 )  B      O      0.41    2.29  INTRA BF
 815 LEU   ( 320-)  B      O   <->  818 ILE   ( 323-)  B      CG1    0.41    2.39  INTRA
 170 LEU   ( 170-)  A      CD2 <->  202 MET   ( 202-)  A      SD     0.41    2.99  INTRA
 722 ARG   ( 227-)  B      CD  <-> 1234 HOH   ( 799 )  B      O      0.40    2.40  INTRA
 887 ARG   ( 392-)  B      O   <->  890 VAL   ( 395-)  B      CG2    0.39    2.41  INTRA
 383 VAL   ( 383-)  A      CG2 <->  385 GLU   ( 385-)  A      OE1    0.39    2.41  INTRA BL
 665 LEU   ( 170-)  B      CD2 <->  697 MET   ( 202-)  B      SD     0.38    3.02  INTRA
1228 SER   ( 120-)  D      C   <-> 1229 SER   ( 121-)  D      C      0.37    2.43  INTRA B3
 497 TYR   (   2-)  B      O   <->  747 ARG   ( 252-)  B      CD     0.37    2.43  INTRA
And so on for a total of 202 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

  72 ARG   (  72-)  A      -6.77
 567 ARG   (  72-)  B      -6.69
1221 GLN   ( 113-)  D      -5.90
 305 HIS   ( 305-)  A      -5.66
 613 TYR   ( 118-)  B      -5.66
1102 GLN   ( 113-)  C      -5.65
 502 GLN   (   7-)  B      -5.59
 779 TRP   ( 284-)  B      -5.49
 284 TRP   ( 284-)  A      -5.47
   7 GLN   (   7-)  A      -5.42
 800 HIS   ( 305-)  B      -5.40
 118 TYR   ( 118-)  A      -5.37
 798 ARG   ( 303-)  B      -5.37
 303 ARG   ( 303-)  A      -5.37
 774 ASN   ( 279-)  B      -5.33
 279 ASN   ( 279-)  A      -5.33
 525 ARG   (  30-)  B      -5.32
  30 ARG   (  30-)  A      -5.32
  53 ASN   (  53-)  A      -5.30
 797 GLN   ( 302-)  B      -5.29
 583 ASN   (  88-)  B      -5.27
 302 GLN   ( 302-)  A      -5.24
 548 ASN   (  53-)  B      -5.20
1097 ILE   ( 108-)  C      -5.16
 762 ARG   ( 267-)  B      -5.10
 267 ARG   ( 267-)  A      -5.10
 696 HIS   ( 201-)  B      -5.06
 201 HIS   ( 201-)  A      -5.03

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

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: D

Warning: Low packing Z-score for some residues

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

 838 ARG   ( 343-)  B   -2.77
 343 ARG   ( 343-)  A   -2.64
 960 ILE   ( 465-)  B   -2.63
 238 GLY   ( 238-)  A   -2.59
 243 LYS   ( 243-)  A   -2.59
 512 PHE   (  17-)  B   -2.55
1137 LEU   (  29-)  D   -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: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

1233 HOH   ( 733 )  A      O     26.85   29.82   55.62
1233 HOH   ( 758 )  A      O     17.31   -0.93   45.78
1233 HOH   ( 799 )  A      O     28.87   28.02   55.52
1233 HOH   ( 802 )  A      O     16.89   20.74   48.77
1233 HOH   ( 875 )  A      O     21.78   32.00   -4.54
1233 HOH   ( 890 )  A      O     32.50   35.40   -2.94
1233 HOH   ( 919 )  A      O     16.22   28.84   54.28
1233 HOH   ( 966 )  A      O     24.06  -16.50  -13.98
1233 HOH   ( 979 )  A      O      8.55   53.34   46.85
1233 HOH   (1004 )  A      O     30.69   25.76   53.67
1233 HOH   (1045 )  A      O     -7.52   14.60  -31.34
1233 HOH   (1068 )  A      O     15.30    3.10   44.77
1234 HOH   ( 667 )  B      O    -11.03   -2.40  -45.50
1234 HOH   ( 896 )  B      O    -21.07    1.20  -42.18
1234 HOH   ( 905 )  B      O    -15.53  -23.96  -53.36
1234 HOH   ( 948 )  B      O     -2.93   -7.26  -44.44
1235 HOH   ( 214 )  C      O      9.29   19.33   -3.39
1236 HOH   ( 203 )  D      O    -23.44  -20.30   -5.91
1236 HOH   ( 219 )  D      O     30.39  -35.90  -13.67
1236 HOH   ( 230 )  D      O    -17.71  -36.40  -12.57
1236 HOH   ( 237 )  D      O     -7.33  -12.69   16.50
1236 HOH   ( 257 )  D      O     17.88  -25.81    1.50
1236 HOH   ( 260 )  D      O    -24.99  -33.69  -14.31
1236 HOH   ( 267 )  D      O    -24.79  -31.99  -12.25

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.

1233 HOH   ( 838 )  A      O
1233 HOH   (1055 )  A      O
1234 HOH   ( 970 )  B      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.

   5 GLN   (   5-)  A
 100 ASN   ( 100-)  A
 101 HIS   ( 101-)  A
 201 HIS   ( 201-)  A
 279 ASN   ( 279-)  A
 299 HIS   ( 299-)  A
 373 ASN   ( 373-)  A
 399 ASN   ( 399-)  A
 500 GLN   (   5-)  B
 596 HIS   ( 101-)  B
 696 HIS   ( 201-)  B
 794 HIS   ( 299-)  B
 894 ASN   ( 399-)  B
1016 ASN   (  27-)  C
1042 ASN   (  53-)  C
1070 GLN   (  81-)  C
1179 GLN   (  71-)  D
1181 ASN   (  73-)  D
1189 GLN   (  81-)  D

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.

  59 TRP   (  59-)  A      N
 101 HIS   ( 101-)  A      N
 138 ASP   ( 138-)  A      N
 182 TYR   ( 182-)  A      OH
 193 GLY   ( 193-)  A      N
 251 GLY   ( 251-)  A      N
 252 ARG   ( 252-)  A      NE
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 316 TRP   ( 316-)  A      NE1
 344 TRP   ( 344-)  A      N
 348 PHE   ( 348-)  A      N
 357 TRP   ( 357-)  A      N
 370 VAL   ( 370-)  A      N
 403 GLY   ( 403-)  A      N
 434 TRP   ( 434-)  A      N
 454 SER   ( 454-)  A      N
 481 ASN   ( 481-)  A      ND2
 554 TRP   (  59-)  B      N
 582 ASN   (  87-)  B      ND2
 596 HIS   ( 101-)  B      N
 670 VAL   ( 175-)  B      N
 677 TYR   ( 182-)  B      OH
 688 GLY   ( 193-)  B      N
 690 ARG   ( 195-)  B      NE
 690 ARG   ( 195-)  B      NH1
 746 GLY   ( 251-)  B      N
 747 ARG   ( 252-)  B      NE
 768 LYS   ( 273-)  B      N
 774 ASN   ( 279-)  B      N
 776 GLY   ( 281-)  B      N
 790 PHE   ( 295-)  B      N
 811 TRP   ( 316-)  B      NE1
 832 ARG   ( 337-)  B      NH1
 832 ARG   ( 337-)  B      NH2
 839 TRP   ( 344-)  B      N
 852 TRP   ( 357-)  B      N
 865 VAL   ( 370-)  B      N
 929 TRP   ( 434-)  B      N
 949 SER   ( 454-)  B      N
 966 SER   ( 471-)  B      OG
 967 ASP   ( 472-)  B      N
1038 SER   (  49-)  C      OG
1089 ARG   ( 100-)  C      NH2
1090 TYR   ( 101-)  C      N
1136 THR   (  28-)  D      OG1
1157 SER   (  49-)  D      OG
1208 ARG   ( 100-)  D      NH2
1209 TYR   ( 101-)  D      N

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

   1 GLN   (   1-)  A      OE1
  15 HIS   (  15-)  A      NE2
 510 HIS   (  15-)  B      NE2
 591 ASP   (  96-)  B      OD1
 995 GLU   (   6-)  C      OE2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1233 HOH   ( 497 )  A      O  1.03 NA  8 *2
1233 HOH   ( 540 )  A      O  0.92  K  4
1233 HOH   ( 547 )  A      O  0.88  K  7
1233 HOH   ( 739 )  A      O  0.90  K  4
1233 HOH   ( 882 )  A      O  0.86  K  5 ION-B
1234 HOH   ( 497 )  B      O  0.97 NA  8 *2
1234 HOH   ( 528 )  B      O  0.98  K  5
1234 HOH   ( 536 )  B      O  1.14  K  7
1234 HOH   ( 580 )  B      O  0.88  K  4
1234 HOH   ( 779 )  B      O  1.04  K  5 ION-B
1234 HOH   ( 788 )  B      O  0.86  K  4 Ion-B
1235 HOH   ( 142 )  C      O  0.97  K  5
1235 HOH   ( 146 )  C      O  0.85  K  4
1236 HOH   ( 159 )  D      O  1.12 CA  4 (or NA *2) ION-B

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.

 167 ASP   ( 167-)  A   H-bonding suggests Asn
 181 ASP   ( 181-)  A   H-bonding suggests Asn
 662 ASP   ( 167-)  B   H-bonding suggests Asn
 847 GLU   ( 352-)  B   H-bonding suggests Gln
 851 ASP   ( 356-)  B   H-bonding suggests Asn
 995 GLU   (   6-)  C   H-bonding suggests Gln; but Alt-Rotamer
1154 ASP   (  46-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.064
  2nd generation packing quality :  -1.921
  Ramachandran plot appearance   :  -0.927
  chi-1/chi-2 rotamer normality  :  -2.047
  Backbone conformation          :  -0.705

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.808
  Bond angles                    :   1.010
  Omega angle restraints         :   0.588 (tight)
  Side chain planarity           :   0.578 (tight)
  Improper dihedral distribution :   1.035
  B-factor distribution          :   0.613
  Inside/Outside distribution    :   0.994

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 : 1.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -2.4
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.808
  Bond angles                    :   1.010
  Omega angle restraints         :   0.588 (tight)
  Side chain planarity           :   0.578 (tight)
  Improper dihedral distribution :   1.035
  B-factor distribution          :   0.613
  Inside/Outside distribution    :   0.994
==============

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.