WHAT IF Check report

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

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

Verification log for pdb2pff.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 43 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 3
Highest polymer chain multiplicity according to SEQRES: 6
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
There is also SEQRES evidence for a multiplicity of: 3
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 24
Polymer chain multiplicity and SEQRES multiplicity disagree 3 6
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very high

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

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 625244.750
Volume of the Unit Cell V= 40353944.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 16.135
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.570 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

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: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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'.

 302 SER   ( 972-)  A      OG
 304 ASP   ( 974-)  A      CG
 304 ASP   ( 974-)  A      OD1
 304 ASP   ( 974-)  A      OD2
 307 TYR   ( 977-)  A      CG
 307 TYR   ( 977-)  A      CD1
 307 TYR   ( 977-)  A      CD2
 307 TYR   ( 977-)  A      CE1
 307 TYR   ( 977-)  A      CE2
 307 TYR   ( 977-)  A      CZ
 307 TYR   ( 977-)  A      OH
 309 PRO   ( 984-)  A      CG
 309 PRO   ( 984-)  A      CD
 310 ARG   ( 985-)  A      CG
 310 ARG   ( 985-)  A      CD
 310 ARG   ( 985-)  A      NE
 310 ARG   ( 985-)  A      CZ
 310 ARG   ( 985-)  A      NH1
 310 ARG   ( 985-)  A      NH2
 312 ASN   ( 987-)  A      CG
 312 ASN   ( 987-)  A      OD1
 312 ASN   ( 987-)  A      ND2
 313 ILE   ( 988-)  A      CG1
 313 ILE   ( 988-)  A      CG2
 313 ILE   ( 988-)  A      CD1
And so on for a total of 192 lines.

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.

   1 VAL   ( 671-)  A    High
   2 THR   ( 672-)  A    High
   3 PHE   ( 673-)  A    High
   4 LYS   ( 674-)  A    High
   5 ASP   ( 675-)  A    High
   6 LYS   ( 676-)  A    High
   7 TYR   ( 677-)  A    High
   8 VAL   ( 678-)  A    High
   9 LEU   ( 679-)  A    High
  10 ILE   ( 680-)  A    High
  11 THR   ( 681-)  A    High
  12 GLY   ( 682-)  A    High
  13 ALA   ( 683-)  A    High
  14 GLY   ( 684-)  A    High
  15 LYS   ( 685-)  A    High
  16 GLY   ( 686-)  A    High
  17 SER   ( 687-)  A    High
  20 ALA   ( 690-)  A    High
  21 GLU   ( 691-)  A    High
  22 VAL   ( 692-)  A    High
  23 LEU   ( 693-)  A    High
  24 GLN   ( 694-)  A    High
  25 GLY   ( 695-)  A    High
  26 LEU   ( 696-)  A    High
  27 LEU   ( 697-)  A    High
And so on for a total of 5152 lines.

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: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Nomenclature related problems

Warning: Tyrosine convention problem

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

   7 TYR   ( 677-)  A
 439 TYR   (1114-)  A
 657 TYR   (1332-)  A
 995 TYR   (1670-)  A
1040 TYR   (1715-)  A
1073 TYR   (   4-)  B
1421 TYR   ( 352-)  B
1627 TYR   (1681-)  B
1679 TYR   (1733-)  B
1758 TYR   (1812-)  B
1779 TYR   (1833-)  B
1894 TYR   ( 677-)  D
2326 TYR   (1114-)  D
2544 TYR   (1332-)  D
2882 TYR   (1670-)  D
2927 TYR   (1715-)  D
2960 TYR   (   4-)  E
3308 TYR   ( 352-)  E
3514 TYR   (1681-)  E
3566 TYR   (1733-)  E
3645 TYR   (1812-)  E
3666 TYR   (1833-)  E
3781 TYR   ( 677-)  G
4213 TYR   (1114-)  G
4431 TYR   (1332-)  G
4769 TYR   (1670-)  G
4814 TYR   (1715-)  G
4847 TYR   (   4-)  H
5195 TYR   ( 352-)  H
5401 TYR   (1681-)  H
5453 TYR   (1733-)  H
5532 TYR   (1812-)  H
5553 TYR   (1833-)  H

Warning: Phenylalanine convention problem

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

   3 PHE   ( 673-)  A
  40 PHE   ( 710-)  A
  67 PHE   ( 737-)  A
 180 PHE   ( 850-)  A
 226 PHE   ( 896-)  A
 548 PHE   (1223-)  A
 586 PHE   (1261-)  A
 810 PHE   (1485-)  A
1097 PHE   (  28-)  B
1106 PHE   (  37-)  B
1327 PHE   ( 258-)  B
1362 PHE   ( 293-)  B
1373 PHE   ( 304-)  B
1565 PHE   ( 496-)  B
1573 PHE   ( 504-)  B
1644 PHE   (1698-)  B
1650 PHE   (1704-)  B
1698 PHE   (1752-)  B
1710 PHE   (1764-)  B
1887 PHE   (1941-)  B
1890 PHE   ( 673-)  D
1927 PHE   ( 710-)  D
1954 PHE   ( 737-)  D
2067 PHE   ( 850-)  D
2113 PHE   ( 896-)  D
And so on for a total of 60 lines.

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.

 115 ASP   ( 785-)  A
 339 ASP   (1014-)  A
 588 ASP   (1263-)  A
 592 ASP   (1267-)  A
 806 ASP   (1481-)  A
1071 ASP   (   2-)  B
2002 ASP   ( 785-)  D
2226 ASP   (1014-)  D
2475 ASP   (1263-)  D
2479 ASP   (1267-)  D
2693 ASP   (1481-)  D
2958 ASP   (   2-)  E
3889 ASP   ( 785-)  G
4113 ASP   (1014-)  G
4362 ASP   (1263-)  G
4366 ASP   (1267-)  G
4580 ASP   (1481-)  G
4845 ASP   (   2-)  H

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.

  76 GLU   ( 746-)  A
 106 GLU   ( 776-)  A
 186 GLU   ( 856-)  A
 377 GLU   (1052-)  A
 419 GLU   (1094-)  A
 453 GLU   (1128-)  A
 454 GLU   (1129-)  A
 481 GLU   (1156-)  A
 484 GLU   (1159-)  A
 546 GLU   (1221-)  A
 602 GLU   (1277-)  A
 642 GLU   (1317-)  A
1840 GLU   (1894-)  B
1963 GLU   ( 746-)  D
1993 GLU   ( 776-)  D
2073 GLU   ( 856-)  D
2264 GLU   (1052-)  D
2306 GLU   (1094-)  D
2340 GLU   (1128-)  D
2341 GLU   (1129-)  D
2368 GLU   (1156-)  D
2371 GLU   (1159-)  D
2433 GLU   (1221-)  D
2489 GLU   (1277-)  D
2529 GLU   (1317-)  D
3727 GLU   (1894-)  E
3850 GLU   ( 746-)  G
3880 GLU   ( 776-)  G
3960 GLU   ( 856-)  G
4151 GLU   (1052-)  G
4193 GLU   (1094-)  G
4227 GLU   (1128-)  G
4228 GLU   (1129-)  G
4255 GLU   (1156-)  G
4258 GLU   (1159-)  G
4320 GLU   (1221-)  G
4376 GLU   (1277-)  G
4416 GLU   (1317-)  G
5614 GLU   (1894-)  H

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.

 450 VAL   (1125-)  A      CA   CB    1.63    5.0
 475 ASP   (1150-)  A      CB   CG    2.20   27.2
 506 PHE   (1181-)  A      CG   CD1   1.57    9.0
 506 PHE   (1181-)  A      CG   CD2   1.57    8.9
 506 PHE   (1181-)  A      CD1  CE1   1.78   13.4
 506 PHE   (1181-)  A      CD2  CE2   1.79   13.6
 506 PHE   (1181-)  A      CE1  CZ    1.75   12.4
 506 PHE   (1181-)  A      CE2  CZ    1.75   12.4
2337 VAL   (1125-)  D      CA   CB    1.63    5.2
2362 ASP   (1150-)  D      CB   CG    2.20   27.3
2393 PHE   (1181-)  D      CG   CD1   1.58    9.3
2393 PHE   (1181-)  D      CG   CD2   1.58    9.3
2393 PHE   (1181-)  D      CD1  CE1   1.78   13.2
2393 PHE   (1181-)  D      CD2  CE2   1.81   14.3
2393 PHE   (1181-)  D      CE1  CZ    1.73   11.6
2393 PHE   (1181-)  D      CE2  CZ    1.74   11.9
4224 VAL   (1125-)  G      CA   CB    1.61    4.2
4249 ASP   (1150-)  G      CB   CG    2.21   27.6
4280 PHE   (1181-)  G      CG   CD1   1.57    8.8
4280 PHE   (1181-)  G      CG   CD2   1.57    8.9
4280 PHE   (1181-)  G      CD1  CE1   1.78   13.3
4280 PHE   (1181-)  G      CD2  CE2   1.80   14.0
4280 PHE   (1181-)  G      CE1  CZ    1.75   12.2
4280 PHE   (1181-)  G      CE2  CZ    1.76   12.7

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

 |  0.999450 -0.000103 -0.000111|
 | -0.000103  0.999428  0.000081|
 | -0.000111  0.000081  0.999430|
Proposed new scale matrix

 |  0.004325  0.000000  0.000000|
 |  0.000000  0.004325  0.000000|
 |  0.000000  0.000000  0.001327|
With corresponding cell

    A    = 231.194  B   = 231.189  C    = 753.718
    Alpha=  90.006  Beta=  90.006  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 231.321  B   = 231.321  C    = 754.148
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 58.832
(Under-)estimated Z-score: 5.653

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.

 226 PHE   ( 896-)  A      N    CA   C   123.96    4.6
 227 SER   ( 897-)  A      N    CA   C    99.29   -4.3
 309 PRO   ( 984-)  A      N    CA   CB  109.66    6.1
 318 PRO   ( 993-)  A     -C    N    CD   96.93   -6.8
 318 PRO   ( 993-)  A      CD   N    CA  105.90   -4.4
 340 LEU   (1015-)  A      N    CA   C   123.32    4.3
 389 ASN   (1064-)  A      N    CA   C    98.96   -4.4
 390 GLY   (1065-)  A      N    CA   C    92.83   -6.8
 391 ASN   (1066-)  A      N    CA   C    99.23   -4.3
 402 ASP   (1077-)  A      N    CA   C    89.72   -7.7
 430 LEU   (1105-)  A      N    CA   C    98.18   -4.6
 433 PRO   (1108-)  A      N    CA   C   127.07    6.1
 434 GLU   (1109-)  A      N    CA   C   122.67    4.1
 436 PHE   (1111-)  A      N    CA   C    97.74   -4.8
 438 GLY   (1113-)  A      N    CA   C    88.38   -8.3
 451 ILE   (1126-)  A      C    CA   CB  100.59   -5.0
 459 PHE   (1134-)  A      N    CA   C    99.72   -4.1
 475 ASP   (1150-)  A      CA   CB   CG  119.69    7.1
 475 ASP   (1150-)  A      CB   CG   OD1 128.76    4.5
 475 ASP   (1150-)  A      OD2  CG   OD1 106.90   -6.7
 486 GLY   (1161-)  A      N    CA   C    99.84   -4.4
 499 TYR   (1174-)  A      N    CA   C    96.27   -5.3
 500 ILE   (1175-)  A      N    CA   C    97.30   -5.0
 501 PRO   (1176-)  A     -C    N    CA  142.78    4.0
 501 PRO   (1176-)  A     -C    N    CD  106.09   -4.6
And so on for a total of 198 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.

  76 GLU   ( 746-)  A
 106 GLU   ( 776-)  A
 115 ASP   ( 785-)  A
 186 GLU   ( 856-)  A
 339 ASP   (1014-)  A
 377 GLU   (1052-)  A
 419 GLU   (1094-)  A
 453 GLU   (1128-)  A
 454 GLU   (1129-)  A
 481 GLU   (1156-)  A
 484 GLU   (1159-)  A
 546 GLU   (1221-)  A
 588 ASP   (1263-)  A
 592 ASP   (1267-)  A
 602 GLU   (1277-)  A
 642 GLU   (1317-)  A
 806 ASP   (1481-)  A
1071 ASP   (   2-)  B
1840 GLU   (1894-)  B
1963 GLU   ( 746-)  D
1993 GLU   ( 776-)  D
2002 ASP   ( 785-)  D
2073 GLU   ( 856-)  D
2226 ASP   (1014-)  D
2264 GLU   (1052-)  D
And so on for a total of 57 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.

 318 PRO   ( 993-)  A      N     13.9    43.04    -2.48
 396 PRO   (1071-)  A      N      6.5    18.92    -2.48
2205 PRO   ( 993-)  D      N     14.6    45.42    -2.48
2283 PRO   (1071-)  D      N      6.5    19.00    -2.48
4092 PRO   ( 993-)  G      N     13.9    43.21    -2.48
4170 PRO   (1071-)  G      N      6.4    18.57    -2.48
The average deviation= 0.860

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.

4562 VAL   (1463-)  G    9.31
2675 VAL   (1463-)  D    9.14
4212 GLY   (1113-)  G    9.13
2325 GLY   (1113-)  D    9.07
 438 GLY   (1113-)  A    9.04
 788 VAL   (1463-)  A    9.02
2476 ARG   (1264-)  D    8.82
2668 GLU   (1456-)  D    8.80
4555 GLU   (1456-)  G    8.72
 781 GLU   (1456-)  A    8.70
 589 ARG   (1264-)  A    8.61
4363 ARG   (1264-)  G    8.60
4164 GLY   (1065-)  G    7.54
2277 GLY   (1065-)  D    7.54
4563 GLU   (1464-)  G    7.52
4771 GLU   (1672-)  G    7.51
 789 GLU   (1464-)  A    7.51
2676 GLU   (1464-)  D    7.49
 997 GLU   (1672-)  A    7.49
 390 GLY   (1065-)  A    7.44
2884 GLU   (1672-)  D    7.31
 402 ASP   (1077-)  A    7.29
4176 ASP   (1077-)  G    7.18
2289 ASP   (1077-)  D    7.13
 668 PHE   (1343-)  A    7.01
And so on for a total of 364 lines.

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 2.118

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -8.093

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.

4631 THR   (1532-)  G    -3.6
2744 THR   (1532-)  D    -3.6
4611 PHE   (1512-)  G    -3.6
 837 PHE   (1512-)  A    -3.6
 857 THR   (1532-)  A    -3.6
2724 PHE   (1512-)  D    -3.6
4680 THR   (1581-)  G    -3.6
 906 THR   (1581-)  A    -3.6
2793 THR   (1581-)  D    -3.6
4296 THR   (1197-)  G    -3.6
2409 THR   (1197-)  D    -3.6
 522 THR   (1197-)  A    -3.6
2842 THR   (1630-)  D    -3.5
 955 THR   (1630-)  A    -3.5
1032 THR   (1707-)  A    -3.5
4806 THR   (1707-)  G    -3.5
2919 THR   (1707-)  D    -3.5
4729 THR   (1630-)  G    -3.5
 127 THR   ( 797-)  A    -3.5
4210 PHE   (1111-)  G    -3.4
2323 PHE   (1111-)  D    -3.4
 734 THR   (1409-)  A    -3.4
 436 PHE   (1111-)  A    -3.4
3901 THR   ( 797-)  G    -3.4
2014 THR   ( 797-)  D    -3.4
And so on for a total of 828 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   4 LYS   ( 674-)  A  Poor phi/psi
   5 ASP   ( 675-)  A  Poor phi/psi
   7 TYR   ( 677-)  A  Poor phi/psi
  12 GLY   ( 682-)  A  Poor phi/psi
  13 ALA   ( 683-)  A  Poor phi/psi
  17 SER   ( 687-)  A  Poor phi/psi
  18 ILE   ( 688-)  A  Poor phi/psi
  31 ALA   ( 701-)  A  Poor phi/psi
  39 ARG   ( 709-)  A  Poor phi/psi
  40 PHE   ( 710-)  A  Poor phi/psi
  41 SER   ( 711-)  A  Poor phi/psi
  45 THR   ( 715-)  A  Poor phi/psi
  46 ASP   ( 716-)  A  Poor phi/psi
  48 TYR   ( 718-)  A  Poor phi/psi
  52 TYR   ( 722-)  A  Poor phi/psi
  53 ALA   ( 723-)  A  Poor phi/psi
  54 LYS   ( 724-)  A  Poor phi/psi
  55 TYR   ( 725-)  A  Poor phi/psi
  58 LYS   ( 728-)  A  Poor phi/psi
  67 PHE   ( 737-)  A  Poor phi/psi
  71 SER   ( 741-)  A  Poor phi/psi
  72 LYS   ( 742-)  A  Poor phi/psi
  73 GLN   ( 743-)  A  Poor phi/psi
  75 VAL   ( 745-)  A  Poor phi/psi
  88 ASN   ( 758-)  A  Poor phi/psi
And so on for a total of 1933 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 : -5.626

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.

 177 GLU   ( 847-)  A    0.33
2064 GLU   ( 847-)  D    0.33
3951 GLU   ( 847-)  G    0.33

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   ( 673-)  A      0
   4 LYS   ( 674-)  A      0
   5 ASP   ( 675-)  A      0
   6 LYS   ( 676-)  A      0
   7 TYR   ( 677-)  A      0
  11 THR   ( 681-)  A      0
  15 LYS   ( 685-)  A      0
  17 SER   ( 687-)  A      0
  18 ILE   ( 688-)  A      0
  31 ALA   ( 701-)  A      0
  39 ARG   ( 709-)  A      0
  40 PHE   ( 710-)  A      0
  41 SER   ( 711-)  A      0
  44 VAL   ( 714-)  A      0
  48 TYR   ( 718-)  A      0
  53 ALA   ( 723-)  A      0
  54 LYS   ( 724-)  A      0
  55 TYR   ( 725-)  A      0
  57 ALA   ( 727-)  A      0
  58 LYS   ( 728-)  A      0
  60 SER   ( 730-)  A      0
  67 PHE   ( 737-)  A      0
  71 SER   ( 741-)  A      0
  73 GLN   ( 743-)  A      0
  88 ASN   ( 758-)  A      0
And so on for a total of 3231 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -2.611

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 : 1.345

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!

4941 GLY   (  98-)  H   3.22   10
3054 GLY   (  98-)  E   3.22   10
1167 GLY   (  98-)  B   3.21   11
2083 GLY   ( 866-)  D   2.28   31
3970 GLY   ( 866-)  G   2.25   29
 196 GLY   ( 866-)  A   2.25   29
3463 GLY   ( 507-)  E   2.21   10
1742 GLY   (1796-)  B   1.95   41
5516 GLY   (1796-)  H   1.95   41
3629 GLY   (1796-)  E   1.94   42
3826 TYR   ( 722-)  G   1.80   23
  52 TYR   ( 722-)  A   1.78   23
1939 TYR   ( 722-)  D   1.78   22
3941 GLY   ( 837-)  G   1.75   14
2054 GLY   ( 837-)  D   1.75   14
 167 GLY   ( 837-)  A   1.72   13
2551 GLY   (1339-)  D   1.69   13
4438 GLY   (1339-)  G   1.68   13
1470 GLY   ( 401-)  B   1.68   15
3357 GLY   ( 401-)  E   1.68   15
5244 GLY   ( 401-)  H   1.67   14
 664 GLY   (1339-)  A   1.64   14
3991 GLY   ( 887-)  G   1.61   80
 217 GLY   ( 887-)  A   1.61   80
 786 ASP   (1461-)  A   1.61   25
2104 GLY   ( 887-)  D   1.61   80
4560 ASP   (1461-)  G   1.60   25
2673 ASP   (1461-)  D   1.59   25
1135 GLY   (  66-)  B   1.59   80
3022 GLY   (  66-)  E   1.58   80
1534 GLY   ( 465-)  B   1.58   28
3421 GLY   ( 465-)  E   1.57   28
4909 GLY   (  66-)  H   1.56   80
5308 GLY   ( 465-)  H   1.56   28
2801 GLY   (1589-)  D   1.50   49
 851 LEU   (1526-)  A   1.50   13

Warning: Unusual peptide bond conformations

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

 225 THR   ( 895-)  A   1.99
 323 TYR   ( 998-)  A   1.58
 493 LEU   (1168-)  A   1.95
 570 ASN   (1245-)  A   1.92
 659 ASP   (1334-)  A   1.68
 733 ALA   (1408-)  A   1.76
1706 THR   (1760-)  B   1.54
2112 THR   ( 895-)  D   1.96
2210 TYR   ( 998-)  D   1.75
2380 LEU   (1168-)  D   2.23
2457 ASN   (1245-)  D   1.88
2572 ARG   (1360-)  D   1.52
2620 ALA   (1408-)  D   1.51
2833 PHE   (1621-)  D   1.53
3999 THR   ( 895-)  G   2.06
4097 TYR   ( 998-)  G   1.67
4267 LEU   (1168-)  G   2.04
4344 ASN   (1245-)  G   2.05
4507 ALA   (1408-)  G   1.55
4720 PHE   (1621-)  G   1.68
5480 THR   (1760-)  H   1.61

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]

 309 PRO   ( 984-)  A    0.00 LOW
 318 PRO   ( 993-)  A    0.47 HIGH
 433 PRO   (1108-)  A    0.47 HIGH
 483 PRO   (1158-)  A    0.45 HIGH
 515 PRO   (1190-)  A    0.46 HIGH
 535 PRO   (1210-)  A    0.45 HIGH
1043 PRO   (1718-)  A    0.00 LOW
2196 PRO   ( 984-)  D    0.00 LOW
2205 PRO   ( 993-)  D    0.47 HIGH
2320 PRO   (1108-)  D    0.47 HIGH
2370 PRO   (1158-)  D    0.45 HIGH
2402 PRO   (1190-)  D    0.46 HIGH
2422 PRO   (1210-)  D    0.45 HIGH
2930 PRO   (1718-)  D    0.00 LOW
4083 PRO   ( 984-)  G    0.00 LOW
4092 PRO   ( 993-)  G    0.47 HIGH
4207 PRO   (1108-)  G    0.47 HIGH
4257 PRO   (1158-)  G    0.45 HIGH
4289 PRO   (1190-)  G    0.46 HIGH
4309 PRO   (1210-)  G    0.45 HIGH
4683 PRO   (1584-)  G    0.46 HIGH
4817 PRO   (1718-)  G    0.00 LOW

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].

 241 PRO   ( 911-)  A  -112.1 envelop C-gamma (-108 degrees)
 318 PRO   ( 993-)  A   148.5 envelop C-alpha (144 degrees)
 354 PRO   (1029-)  A  -119.8 half-chair C-delta/C-gamma (-126 degrees)
 396 PRO   (1071-)  A   131.4 half-chair C-beta/C-alpha (126 degrees)
 441 PRO   (1116-)  A   -59.2 half-chair C-beta/C-alpha (-54 degrees)
 458 PRO   (1133-)  A    40.6 envelop C-delta (36 degrees)
 501 PRO   (1176-)  A   -61.1 half-chair C-beta/C-alpha (-54 degrees)
 515 PRO   (1190-)  A   -59.7 half-chair C-beta/C-alpha (-54 degrees)
 556 PRO   (1231-)  A  -114.1 envelop C-gamma (-108 degrees)
 622 PRO   (1297-)  A   -65.6 envelop C-beta (-72 degrees)
 746 PRO   (1421-)  A   103.7 envelop C-beta (108 degrees)
 766 PRO   (1441-)  A   -54.0 half-chair C-beta/C-alpha (-54 degrees)
 842 PRO   (1517-)  A  -112.1 envelop C-gamma (-108 degrees)
 846 PRO   (1521-)  A   -61.5 half-chair C-beta/C-alpha (-54 degrees)
 931 PRO   (1606-)  A   -59.2 half-chair C-beta/C-alpha (-54 degrees)
 952 PRO   (1627-)  A   110.0 envelop C-beta (108 degrees)
1329 PRO   ( 260-)  B  -118.8 half-chair C-delta/C-gamma (-126 degrees)
1477 PRO   ( 408-)  B   -65.3 envelop C-beta (-72 degrees)
1606 PRO   ( 537-)  B    99.8 envelop C-beta (108 degrees)
1725 PRO   (1779-)  B   102.2 envelop C-beta (108 degrees)
2205 PRO   ( 993-)  D   148.7 envelop C-alpha (144 degrees)
2241 PRO   (1029-)  D  -120.0 half-chair C-delta/C-gamma (-126 degrees)
2283 PRO   (1071-)  D   131.9 half-chair C-beta/C-alpha (126 degrees)
2328 PRO   (1116-)  D   -59.8 half-chair C-beta/C-alpha (-54 degrees)
2345 PRO   (1133-)  D    40.6 envelop C-delta (36 degrees)
And so on for a total of 56 lines.

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.

2795 HIS   (1583-)  D      ND1 <-> 2797 LYS   (1585-)  D      N      0.77    2.23  INTRA BL
4682 HIS   (1583-)  G      ND1 <-> 4684 LYS   (1585-)  G      N      0.76    2.24  INTRA BL
 908 HIS   (1583-)  A      ND1 <->  910 LYS   (1585-)  A      N      0.73    2.27  INTRA BL
 442 GLU   (1117-)  A      O   <->  444 LYS   (1119-)  A      N      0.68    2.02  INTRA BL
 953 SER   (1628-)  A      O   <->  955 THR   (1630-)  A      N      0.67    2.03  INTRA BF
2840 SER   (1628-)  D      O   <-> 2842 THR   (1630-)  D      N      0.66    2.04  INTRA BF
4727 SER   (1628-)  G      O   <-> 4729 THR   (1630-)  G      N      0.65    2.05  INTRA BF
 536 ILE   (1211-)  A      O   <->  538 LEU   (1213-)  A      N      0.64    2.06  INTRA BL
4216 GLU   (1117-)  G      O   <-> 4218 LYS   (1119-)  G      N      0.63    2.07  INTRA BL
4310 ILE   (1211-)  G      O   <-> 4312 LEU   (1213-)  G      N      0.63    2.07  INTRA BL
2423 ILE   (1211-)  D      O   <-> 2425 LEU   (1213-)  D      N      0.62    2.08  INTRA BL
4162 HIS   (1063-)  G      C   <-> 4164 GLY   (1065-)  G      N      0.62    2.28  INTRA BF
2275 HIS   (1063-)  D      C   <-> 2277 GLY   (1065-)  D      N      0.62    2.28  INTRA BF
 388 HIS   (1063-)  A      C   <->  390 GLY   (1065-)  A      N      0.62    2.28  INTRA BF
2329 GLU   (1117-)  D      O   <-> 2331 LYS   (1119-)  D      N      0.60    2.10  INTRA BL
4353 VAL   (1254-)  G      O   <-> 4355 ALA   (1256-)  G      N      0.58    2.12  INTRA BL
4212 GLY   (1113-)  G      N   <-> 4213 TYR   (1114-)  G      N      0.57    2.03  INTRA BL
2401 ILE   (1189-)  D      CG2 <-> 2589 MET   (1377-)  D      SD     0.56    2.84  INTRA BL
 579 VAL   (1254-)  A      O   <->  581 ALA   (1256-)  A      N      0.56    2.14  INTRA BL
2325 GLY   (1113-)  D      N   <-> 2326 TYR   (1114-)  D      N      0.56    2.04  INTRA BL
 514 ILE   (1189-)  A      CG2 <->  702 MET   (1377-)  A      SD     0.56    2.84  INTRA BL
 438 GLY   (1113-)  A      N   <->  439 TYR   (1114-)  A      N      0.56    2.04  INTRA BL
 689 GLU   (1364-)  A      O   <->  691 SER   (1366-)  A      N      0.55    2.15  INTRA BL
2245 ALA   (1033-)  D      O   <-> 2247 THR   (1035-)  D      N      0.55    2.15  INTRA BL
4132 ALA   (1033-)  G      O   <-> 4134 THR   (1035-)  G      N      0.55    2.15  INTRA BL
And so on for a total of 7539 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: D

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: H

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.

4515 ARG   (1416-)  G      -8.73
 741 ARG   (1416-)  A      -8.72
2628 ARG   (1416-)  D      -8.69
 488 TYR   (1163-)  A      -8.30
2375 TYR   (1163-)  D      -8.30
4262 TYR   (1163-)  G      -8.29
1807 ARG   (1861-)  B      -7.95
3694 ARG   (1861-)  E      -7.93
5581 ARG   (1861-)  H      -7.91
1926 ARG   ( 709-)  D      -7.67
3813 ARG   ( 709-)  G      -7.67
  39 ARG   ( 709-)  A      -7.66
2284 TYR   (1072-)  D      -7.49
4171 TYR   (1072-)  G      -7.48
1475 ARG   ( 406-)  B      -7.48
 397 TYR   (1072-)  A      -7.47
5249 ARG   ( 406-)  H      -7.46
3362 ARG   ( 406-)  E      -7.37
4459 ARG   (1360-)  G      -7.27
2572 ARG   (1360-)  D      -7.26
 685 ARG   (1360-)  A      -7.23
 763 TYR   (1438-)  A      -7.16
2650 TYR   (1438-)  D      -7.16
4537 TYR   (1438-)  G      -7.15
3937 PHE   ( 833-)  G      -7.09
And so on for a total of 282 lines.

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.

  38 SER   ( 708-)  A        40 - PHE    710- ( A)         -5.91
 315 LEU   ( 990-)  A       317 - PHE    992- ( A)         -5.83
 391 ASN   (1066-)  A       393 - LYS   1068- ( A)         -4.72
 741 ARG   (1416-)  A       743 - VAL   1418- ( A)         -5.81
 761 VAL   (1436-)  A       763 - TYR   1438- ( A)         -6.04
1026 LYS   (1701-)  A      1028 - HIS   1703- ( A)         -4.93
1480 GLU   ( 411-)  B      1482 - LYS    413- ( B)         -4.62
1588 ASN   ( 519-)  B      1591 - GLY    522- ( B)         -4.59
1806 GLY   (1860-)  B      1808 - VAL   1862- ( B)         -5.57
1925 SER   ( 708-)  D      1927 - PHE    710- ( D)         -5.94
2202 LEU   ( 990-)  D      2204 - PHE    992- ( D)         -5.84
2278 ASN   (1066-)  D      2280 - LYS   1068- ( D)         -4.74
2628 ARG   (1416-)  D      2630 - VAL   1418- ( D)         -5.81
2648 VAL   (1436-)  D      2650 - TYR   1438- ( D)         -6.04
2913 LYS   (1701-)  D      2915 - HIS   1703- ( D)         -4.93
3367 GLU   ( 411-)  E      3369 - LYS    413- ( E)         -4.58
3475 ASN   ( 519-)  E      3478 - GLY    522- ( E)         -4.59
3693 GLY   (1860-)  E      3695 - VAL   1862- ( E)         -5.57
3812 SER   ( 708-)  G      3814 - PHE    710- ( G)         -5.92
4089 LEU   ( 990-)  G      4091 - PHE    992- ( G)         -5.85
4165 ASN   (1066-)  G      4167 - LYS   1068- ( G)         -4.69
4515 ARG   (1416-)  G      4517 - VAL   1418- ( G)         -5.82
4535 VAL   (1436-)  G      4537 - TYR   1438- ( G)         -6.05
4800 LYS   (1701-)  G      4802 - HIS   1703- ( G)         -4.91
5254 GLU   ( 411-)  H      5256 - LYS    413- ( H)         -4.58
5362 ASN   ( 519-)  H      5365 - GLY    522- ( H)         -4.58
5580 GLY   (1860-)  H      5582 - VAL   1862- ( H)         -5.56

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 5661 : -2.209

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: D

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: H

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.

4086 ASN   ( 987-)  G   -3.79
 312 ASN   ( 987-)  A   -3.78
2199 ASN   ( 987-)  D   -3.78
 314 GLN   ( 989-)  A   -3.70
2201 GLN   ( 989-)  D   -3.69
4088 GLN   ( 989-)  G   -3.69
1044 LEU   (1719-)  A   -3.58
2931 LEU   (1719-)  D   -3.57
4818 LEU   (1719-)  G   -3.57
4092 PRO   ( 993-)  G   -3.32
2205 PRO   ( 993-)  D   -3.32
 318 PRO   ( 993-)  A   -3.31
2830 LEU   (1618-)  D   -3.08
4717 LEU   (1618-)  G   -3.08
 943 LEU   (1618-)  A   -3.08
 307 TYR   ( 977-)  A   -3.06
2194 TYR   ( 977-)  D   -3.06
4081 TYR   ( 977-)  G   -3.06
4815 LEU   (1716-)  G   -3.04
2928 LEU   (1716-)  D   -3.00
1041 LEU   (1716-)  A   -2.99
 768 LEU   (1443-)  A   -2.97
4542 LEU   (1443-)  G   -2.95
2655 LEU   (1443-)  D   -2.95
4373 ILE   (1274-)  G   -2.94
And so on for a total of 65 lines.

Warning: Abnormal packing Z-score for sequential residues

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

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

 311 ALA   ( 986-)  A     -  314 GLN   ( 989-)  A        -2.65
 598 ASP   (1273-)  A     -  602 GLU   (1277-)  A        -2.09
 902 GLN   (1577-)  A     -  906 THR   (1581-)  A        -2.01
 933 ASN   (1608-)  A     -  936 ALA   (1611-)  A        -2.13
1039 VAL   (1714-)  A     - 1044 LEU   (1719-)  A        -2.24
1048 SER   (1723-)  A     - 1052 LYS   (1727-)  A        -1.94
2198 ALA   ( 986-)  D     - 2201 GLN   ( 989-)  D        -2.65
2485 ASP   (1273-)  D     - 2489 GLU   (1277-)  D        -2.09
2789 GLN   (1577-)  D     - 2793 THR   (1581-)  D        -2.00
2820 ASN   (1608-)  D     - 2823 ALA   (1611-)  D        -2.00
2926 VAL   (1714-)  D     - 2931 LEU   (1719-)  D        -2.26
2935 SER   (1723-)  D     - 2939 LYS   (1727-)  D        -1.94
4085 ALA   ( 986-)  G     - 4088 GLN   ( 989-)  G        -2.50
4372 ASP   (1273-)  G     - 4376 GLU   (1277-)  G        -2.11
4676 GLN   (1577-)  G     - 4680 THR   (1581-)  G        -2.01
4707 ASN   (1608-)  G     - 4710 ALA   (1611-)  G        -2.11
4813 VAL   (1714-)  G     - 4818 LEU   (1719-)  G        -2.26
4822 SER   (1723-)  G     - 4826 LYS   (1727-)  G        -1.94

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: D

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: H

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  69 GLN   ( 739-)  A
 160 HIS   ( 830-)  A
 191 GLN   ( 861-)  A
 257 ASN   ( 927-)  A
 261 GLN   ( 931-)  A
 472 GLN   (1147-)  A
 532 GLN   (1207-)  A
 820 ASN   (1495-)  A
 874 ASN   (1549-)  A
 902 GLN   (1577-)  A
 973 GLN   (1648-)  A
1224 GLN   ( 155-)  B
1232 GLN   ( 163-)  B
1247 GLN   ( 178-)  B
1314 GLN   ( 245-)  B
1385 ASN   ( 316-)  B
1434 GLN   ( 365-)  B
1459 ASN   ( 390-)  B
1487 ASN   ( 418-)  B
1509 ASN   ( 440-)  B
1618 GLN   (1672-)  B
1956 GLN   ( 739-)  D
2047 HIS   ( 830-)  D
2077 ASN   ( 860-)  D
2078 GLN   ( 861-)  D
And so on for a total of 69 lines.

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 ASP   ( 675-)  A      N
   6 LYS   ( 676-)  A      N
   7 TYR   ( 677-)  A      N
  12 GLY   ( 682-)  A      N
  18 ILE   ( 688-)  A      N
  32 LYS   ( 702-)  A      N
  36 THR   ( 706-)  A      OG1
  39 ARG   ( 709-)  A      N
  49 GLN   ( 719-)  A      N
  53 ALA   ( 723-)  A      N
  69 GLN   ( 739-)  A      NE2
  72 LYS   ( 742-)  A      N
  73 GLN   ( 743-)  A      N
  76 GLU   ( 746-)  A      N
  86 GLU   ( 756-)  A      N
  87 LYS   ( 757-)  A      N
  90 GLY   ( 760-)  A      N
  94 ASP   ( 764-)  A      N
  95 LEU   ( 765-)  A      N
 106 GLU   ( 776-)  A      N
 109 ILE   ( 779-)  A      N
 112 GLU   ( 782-)  A      N
 115 ASP   ( 785-)  A      N
 122 HIS   ( 792-)  A      NE2
 128 ASN   ( 798-)  A      ND2
And so on for a total of 1429 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.

  74 ASP   ( 744-)  A      OD2
 106 GLU   ( 776-)  A      OE2
 248 GLN   ( 918-)  A      OE1
 351 GLU   (1026-)  A      OE1
 402 ASP   (1077-)  A      OD2
 413 ASP   (1088-)  A      OD2
 419 GLU   (1094-)  A      OE2
 445 GLU   (1120-)  A      OE2
 464 GLU   (1139-)  A      OE1
 475 ASP   (1150-)  A      OD2
 481 GLU   (1156-)  A      OE1
 481 GLU   (1156-)  A      OE2
 519 ASN   (1194-)  A      OD1
 570 ASN   (1245-)  A      OD1
 602 GLU   (1277-)  A      OE1
 606 ASN   (1281-)  A      OD1
 613 ASN   (1288-)  A      OD1
 635 GLU   (1310-)  A      OE2
 638 ASP   (1313-)  A      OD2
 659 ASP   (1334-)  A      OD1
 663 GLU   (1338-)  A      OE2
 667 GLU   (1342-)  A      OE1
 689 GLU   (1364-)  A      OE2
 737 ASP   (1412-)  A      OD1
 737 ASP   (1412-)  A      OD2
And so on for a total of 153 lines.

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.

  46 ASP   ( 716-)  A   H-bonding suggests Asn
  74 ASP   ( 744-)  A   H-bonding suggests Asn
 219 GLU   ( 889-)  A   H-bonding suggests Gln
 242 GLU   ( 912-)  A   H-bonding suggests Gln
 255 ASP   ( 925-)  A   H-bonding suggests Asn
 316 ASP   ( 991-)  A   H-bonding suggests Asn; but Alt-Rotamer
 363 GLU   (1038-)  A   H-bonding suggests Gln; but Alt-Rotamer
 373 GLU   (1048-)  A   H-bonding suggests Gln; but Alt-Rotamer
 410 ASP   (1085-)  A   H-bonding suggests Asn
 460 GLU   (1135-)  A   H-bonding suggests Gln
 464 GLU   (1139-)  A   H-bonding suggests Gln
 481 GLU   (1156-)  A   H-bonding suggests Gln
 528 ASP   (1203-)  A   H-bonding suggests Asn; but Alt-Rotamer
 534 ASP   (1209-)  A   H-bonding suggests Asn
 638 ASP   (1313-)  A   H-bonding suggests Asn; but Alt-Rotamer
 716 ASP   (1391-)  A   H-bonding suggests Asn
 737 ASP   (1412-)  A   H-bonding suggests Asn
 756 GLU   (1431-)  A   H-bonding suggests Gln
 786 ASP   (1461-)  A   H-bonding suggests Asn
 821 GLU   (1496-)  A   H-bonding suggests Gln
 878 GLU   (1553-)  A   H-bonding suggests Gln
1006 GLU   (1681-)  A   H-bonding suggests Gln
1027 GLU   (1702-)  A   H-bonding suggests Gln
1086 GLU   (  17-)  B   H-bonding suggests Gln
1122 GLU   (  53-)  B   H-bonding suggests Gln
And so on for a total of 120 lines.

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 :  -4.273 (poor)
  2nd generation packing quality :  -4.545 (bad)
  Ramachandran plot appearance   :  -8.093 (bad)
  chi-1/chi-2 rotamer normality  :  -5.626 (bad)
  Backbone conformation          :  -2.611

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.447 (tight)
  Bond angles                    :   0.835
  Omega angle restraints         :   0.245 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.763
  B-factor distribution          :   1.248
  Inside/Outside distribution    :   1.121

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 : 4.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.7
  2nd generation packing quality :  -2.0
  Ramachandran plot appearance   :  -4.6 (bad)
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.447 (tight)
  Bond angles                    :   0.835
  Omega angle restraints         :   0.245 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.763
  B-factor distribution          :   1.248
  Inside/Outside distribution    :   1.121
==============

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.