WHAT IF Check report

This file was created 2012-04-20 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 pdb3oaa.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 : 1.771
CA-only RMS fit for the two chains : 1.267

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: A and C

All-atom RMS fit for the two chains : 2.099
CA-only RMS fit for the two chains : 1.718

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and I

All-atom RMS fit for the two chains : 0.191
CA-only RMS fit for the two chains : 0.065

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and I

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and J

All-atom RMS fit for the two chains : 1.772
CA-only RMS fit for the two chains : 1.270

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 J

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and K

All-atom RMS fit for the two chains : 2.100
CA-only RMS fit for the two chains : 1.719

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and K

Warning: 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: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 12
Highest polymer chain multiplicity according to SEQRES: 8
There is also SEQRES evidence for a multiplicity of: 12
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 48
Polymer chain multiplicity and SEQRES multiplicity disagree 12 8
Z and NCS seem to support the 3D multiplicity

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1302  ANP  ( 600-) A  -
1303  ANP  ( 600-) B  -
1303  ANP  ( 600-) C  -
1303  ADP  ( 600-) D  -          OK
1304  ANP  ( 600-) I  -
1304  ANP  ( 600-) J  -
1304  ANP  ( 600-) K  -
1304  ADP  ( 600-) L  -          OK
1305  ANP  ( 600-) Q  -
1305  ANP  ( 600-) R  -
1305  ANP  ( 600-) S  -
1306  ADP  ( 600-) T  -          OK
1306  ANP  ( 600-) Y  -
1306  ANP  ( 600-) Z  -
1307  ADP  ( 600-) B  -          OK
1307  ADP  ( 600-) A  -          OK

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

4679 LEU   ( 472-)  K  -
7936 LEU   ( 472-)  S  -

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'.

   1 GLU   (  24-)  A  -   CG
   1 GLU   (  24-)  A  -   CD
   1 GLU   (  24-)  A  -   OE1
   1 GLU   (  24-)  A  -   OE2
 425 LEU   ( 448-)  A  -   CG
 425 LEU   ( 448-)  A  -   CD1
 425 LEU   ( 448-)  A  -   CD2
 441 ILE   ( 464-)  A  -   CG1
 441 ILE   ( 464-)  A  -   CG2
 441 ILE   ( 464-)  A  -   CD1
 869 PHE   ( 406-)  B  -   CG
 869 PHE   ( 406-)  B  -   CD1
 869 PHE   ( 406-)  B  -   CD2
 869 PHE   ( 406-)  B  -   CE1
 869 PHE   ( 406-)  B  -   CE2
 869 PHE   ( 406-)  B  -   CZ
 870 SER   ( 407-)  B  -   OG
 871 GLN   ( 408-)  B  -   CG
 871 GLN   ( 408-)  B  -   CD
 871 GLN   ( 408-)  B  -   OE1
 871 GLN   ( 408-)  B  -   NE2
 874 SER   ( 411-)  B  -   OG
 875 ASP   ( 412-)  B  -   CG
 875 ASP   ( 412-)  B  -   OD1
 875 ASP   ( 412-)  B  -   OD2
And so on for a total of 300 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 GLU   (  24-)  A  -   High
   2 ALA   (  25-)  A  -   High
   3 HIS   (  26-)  A  -   High
   4 ASN   (  27-)  A  -   High
   5 GLU   (  28-)  A  -   High
  12 SER   (  35-)  A  -   High
  13 ASP   (  36-)  A  -   High
  17 ARG   (  40-)  A  -   High
  18 ILE   (  41-)  A  -   High
  19 HIS   (  42-)  A  -   High
  22 ALA   (  45-)  A  -   High
  23 ASP   (  46-)  A  -   High
  24 CYS   (  47-)  A  -   High
  26 GLN   (  49-)  A  -   High
  27 GLY   (  50-)  A  -   High
  28 GLU   (  51-)  A  -   High
  31 SER   (  54-)  A  -   High
  34 GLY   (  57-)  A  -   High
  35 ASN   (  58-)  A  -   High
  36 ARG   (  59-)  A  -   High
  37 TYR   (  60-)  A  -   High
  44 GLU   (  67-)  A  -   High
  45 ARG   (  68-)  A  -   High
  46 ASP   (  69-)  A  -   High
  47 SER   (  70-)  A  -   High
And so on for a total of 9528 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 96

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

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 395 ARG   ( 418-)  A  -
 556 ARG   (  93-)  B  -
 624 ARG   ( 161-)  B  -
 715 ARG   ( 252-)  B  -
 839 ARG   ( 376-)  B  -
2919 ARG   (  84-)  G  -
3056 ARG   ( 221-)  G  -
3248 ARG   ( 129-)  H  -
3652 ARG   ( 418-)  I  -
3813 ARG   (  93-)  J  -
3881 ARG   ( 161-)  J  -
3972 ARG   ( 252-)  J  -
4096 ARG   ( 376-)  J  -
6176 ARG   (  84-)  O  -
6313 ARG   ( 221-)  O  -
6505 ARG   ( 129-)  P  -
6909 ARG   ( 418-)  Q  -
7070 ARG   (  93-)  R  -
7138 ARG   ( 161-)  R  -
7229 ARG   ( 252-)  R  -
7353 ARG   ( 376-)  R  -
9433 ARG   (  84-)  W  -
9570 ARG   ( 221-)  W  -
9762 ARG   ( 129-)  X  -
1016  ARG  ( 418-) Y  -
1032  ARG  (  93-) Z  -
1039  ARG  ( 161-) Z  -
1048  ARG  ( 252-) Z  -
1061  ARG  ( 376-) Z  -
1269  ARG  (  84-) E  -
1282  ARG  ( 221-) E  -
1301  ARG  ( 129-) F  -

Warning: Tyrosine convention problem

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

  56 TYR   (  79-)  A  -
 127 TYR   ( 150-)  A  -
 172 TYR   ( 195-)  A  -
 213 TYR   ( 236-)  A  -
 217 TYR   ( 240-)  A  -
 269 TYR   ( 292-)  A  -
 413 TYR   ( 436-)  A  -
 432 TYR   ( 455-)  A  -
 451 TYR   ( 474-)  A  -
 523 TYR   (  60-)  B  -
 542 TYR   (  79-)  B  -
 711 TYR   ( 248-)  B  -
 755 TYR   ( 292-)  B  -
 863 TYR   ( 400-)  B  -
 899 TYR   ( 436-)  B  -
 918 TYR   ( 455-)  B  -
 937 TYR   ( 474-)  B  -
 955 TYR   ( 492-)  B  -
1029 TYR   (  79-)  C  -
1100 TYR   ( 150-)  C  -
1145 TYR   ( 195-)  C  -
1190 TYR   ( 240-)  C  -
1210 TYR   ( 260-)  C  -
1242 TYR   ( 292-)  C  -
1258 TYR   ( 308-)  C  -
And so on for a total of 211 lines.

Warning: Phenylalanine convention problem

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

 226 PHE   ( 249-)  A  -
 263 PHE   ( 286-)  A  -
 289 PHE   ( 312-)  A  -
 317 PHE   ( 340-)  A  -
 484 PHE   ( 507-)  A  -
 712 PHE   ( 249-)  B  -
 775 PHE   ( 312-)  B  -
 803 PHE   ( 340-)  B  -
 823 PHE   ( 360-)  B  -
 872 PHE   ( 409-)  B  -
 970 PHE   ( 507-)  B  -
1199 PHE   ( 249-)  C  -
1290 PHE   ( 340-)  C  -
1356 PHE   ( 406-)  C  -
1359 PHE   ( 409-)  C  -
1457 PHE   ( 507-)  C  -
1477 PHE   (  17-)  D  -
1864 PHE   ( 404-)  D  -
1865 PHE   ( 405-)  D  -
1887 PHE   ( 427-)  D  -
1935 PHE   (  17-)  E  -
2094 PHE   ( 176-)  E  -
2148 PHE   ( 230-)  E  -
2322 PHE   ( 404-)  E  -
2328 PHE   ( 410-)  E  -
And so on for a total of 154 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.

  46 ASP   (  69-)  A  -
  58 ASP   (  81-)  A  -
 101 ASP   ( 124-)  A  -
 131 ASP   ( 154-)  A  -
 158 ASP   ( 181-)  A  -
 165 ASP   ( 188-)  A  -
 228 ASP   ( 251-)  A  -
 239 ASP   ( 262-)  A  -
 266 ASP   ( 289-)  A  -
 327 ASP   ( 350-)  A  -
 389 ASP   ( 412-)  A  -
 391 ASP   ( 414-)  A  -
 392 ASP   ( 415-)  A  -
 399 ASP   ( 422-)  A  -
 435 ASP   ( 458-)  A  -
 544 ASP   (  81-)  B  -
 579 ASP   ( 116-)  B  -
 617 ASP   ( 154-)  B  -
 644 ASP   ( 181-)  B  -
 714 ASP   ( 251-)  B  -
 718 ASP   ( 255-)  B  -
 752 ASP   ( 289-)  B  -
 813 ASP   ( 350-)  B  -
 885 ASP   ( 422-)  B  -
 939 ASP   ( 476-)  B  -
And so on for a total of 327 lines.

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.

  61 GLU   (  84-)  A  -
 107 GLU   ( 130-)  A  -
 190 GLU   ( 213-)  A  -
 191 GLU   ( 214-)  A  -
 224 GLU   ( 247-)  A  -
 276 GLU   ( 299-)  A  -
 287 GLU   ( 310-)  A  -
 293 GLU   ( 316-)  A  -
 379 GLU   ( 402-)  A  -
 437 GLU   ( 460-)  A  -
 462 GLU   ( 485-)  A  -
 530 GLU   (  67-)  B  -
 677 GLU   ( 214-)  B  -
 747 GLU   ( 284-)  B  -
 762 GLU   ( 299-)  B  -
 770 GLU   ( 307-)  B  -
 865 GLU   ( 402-)  B  -
 915 GLU   ( 452-)  B  -
 958 GLU   ( 495-)  B  -
1017 GLU   (  67-)  C  -
1080 GLU   ( 130-)  C  -
1164 GLU   ( 214-)  C  -
1234 GLU   ( 284-)  C  -
1249 GLU   ( 299-)  C  -
1410 GLU   ( 460-)  C  -
And so on for a total of 342 lines.

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): A, B, C, D, E, F

Geometric checks

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

 |  0.999724 -0.000008 -0.000022|
 | -0.000008  0.999697  0.000003|
 | -0.000022  0.000003  0.999756|
Proposed new scale matrix

 |  0.002295  0.000000  0.000789|
 |  0.000000  0.005466  0.000000|
 |  0.000000  0.000000  0.004693|
With corresponding cell

    A    = 435.799  B   = 182.961  C    = 225.330
    Alpha=  90.001  Beta= 108.982  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 435.920  B   = 183.016  C    = 225.383
    Alpha=  90.000  Beta= 108.980  Gamma=  90.000

Variance: 30.716
(Under-)estimated Z-score: 4.085

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.

 155 LEU   ( 178-)  A  -   N    CA   C    96.85   -5.1
 871 GLN   ( 408-)  B  -   N    CA   C   127.54    5.8
1412 SER   ( 462-)  C  -  -C    N    CA  130.93    5.1
1572 ALA   ( 112-)  D  -   N    CA   C    98.84   -4.4
1572 ALA   ( 112-)  D  -   C    CA   CB  118.07    5.0
2532 THR   ( 156-)  F  -   C    CA   CB  101.02   -4.8
3120 ALA   (   1-)  H  -   N    CA   C    90.24   -7.5
3120 ALA   (   1-)  H  -   C    CA   CB  151.29   27.2
3371 ILE   ( 137-)  I  -   N    CA   CB  117.47    4.1
3372 GLU   ( 138-)  I  -  -C    N    CA  108.32   -7.4
3372 GLU   ( 138-)  I  -   N    CA   C   129.34    6.5
3410 THR   ( 176-)  I  -   N    CA   C    98.76   -4.4
3412 LEU   ( 178-)  I  -   N    CA   C    98.80   -4.4
3692 ASP   ( 458-)  I  -   N    CA   C   122.79    4.1
4128 GLN   ( 408-)  J  -   N    CA   C   127.52    5.8
4669 SER   ( 462-)  K  -  -C    N    CA  130.94    5.1
4829 ALA   ( 112-)  L  -   N    CA   C    95.98   -5.4
4829 ALA   ( 112-)  L  -   C    CA   CB  122.06    7.7
5506 TYR   ( 331-)  M  -   N    CA   C   122.49    4.0
5789 THR   ( 156-)  N  -   C    CA   CB   99.86   -5.4
6434 HIS   (  58-)  P  -   CG   ND1  CE1 109.64    4.0
6628 ILE   ( 137-)  Q  -   C    CA   CB  100.69   -5.0
7385 GLN   ( 408-)  R  -   N    CA   C   130.80    7.0
7386 PHE   ( 409-)  R  -  -C    N    CA  129.80    4.5
7926 SER   ( 462-)  S  -  -C    N    CA  130.93    5.1
7995 ALA   (  21-)  T  -   N    CA   C    96.79   -5.1
8086 ALA   ( 112-)  T  -   N    CA   C    93.57   -6.3
8086 ALA   ( 112-)  T  -   C    CA   CB  126.10   10.4
9046 THR   ( 156-)  V  -   C    CA   CB  102.44   -4.0
9540 PRO   ( 191-)  W  -  -C    N    CD  106.47   -4.5
9885 ILE   ( 137-)  Y  -   N    CA   C   143.09   11.4
9886 GLU   ( 138-)  Y  -  -C    N    CA   80.11  -23.1
9925 ALA   ( 177-)  Y  -   N    CA   CB  116.56    4.1
1033  VAL  (  97-) Z  -   -C    N    CA  113.10   -4.8
1064  GLN  ( 408-) Z  -    N    CA   C   127.55    5.8
1118  SER  ( 462-) A  -   -C    N    CA  130.92    5.1
1125  ALA  (  21-) B  -    N    CA   C    96.75   -5.2
1222  HIS  (  73-) D  -    CG   ND1  CE1 109.63    4.0
1279  PRO  ( 191-) E  -   -C    N    CD   86.52   -9.4
1289  ALA  (   1-) F  -    N    CA   C    90.28   -7.5
1289  ALA  (   1-) F  -    C    CA   CB  151.26   27.2
1299  HIS  ( 109-) F  -    CG   ND1  CE1 109.65    4.0

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.

  46 ASP   (  69-)  A  -
  58 ASP   (  81-)  A  -
  61 GLU   (  84-)  A  -
 101 ASP   ( 124-)  A  -
 107 GLU   ( 130-)  A  -
 131 ASP   ( 154-)  A  -
 158 ASP   ( 181-)  A  -
 165 ASP   ( 188-)  A  -
 190 GLU   ( 213-)  A  -
 191 GLU   ( 214-)  A  -
 224 GLU   ( 247-)  A  -
 228 ASP   ( 251-)  A  -
 239 ASP   ( 262-)  A  -
 266 ASP   ( 289-)  A  -
 276 GLU   ( 299-)  A  -
 287 GLU   ( 310-)  A  -
 293 GLU   ( 316-)  A  -
 327 ASP   ( 350-)  A  -
 379 GLU   ( 402-)  A  -
 389 ASP   ( 412-)  A  -
 391 ASP   ( 414-)  A  -
 392 ASP   ( 415-)  A  -
 395 ARG   ( 418-)  A  -
 399 ASP   ( 422-)  A  -
 435 ASP   ( 458-)  A  -
And so on for a total of 701 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.

 112 GLY   ( 135-)  A  -   C      6.9     9.15     0.06
2264 PRO   ( 346-)  E  -   N      6.3    18.20    -2.48
2394 PRO   (  18-)  F  -   N      7.4    21.64    -2.48
3024 PRO   ( 189-)  G  -   N     -9.4   -33.21    -2.48
3120 ALA   (   1-)  H  -   CA   -17.5    11.92    34.09
3371 ILE   ( 137-)  I  -   C      7.1     9.35     0.03
3372 GLU   ( 138-)  I  -   CA   -15.9     7.90    33.96
3814 ILE   (  94-)  J  -   C     10.0    13.07     0.03
5651 PRO   (  18-)  N  -   N      7.3    21.62    -2.48
6281 PRO   ( 189-)  O  -   N     -9.3   -33.03    -2.48
6283 PRO   ( 191-)  O  -   N     -7.1   -25.77    -2.48
8908 PRO   (  18-)  V  -   N      7.4    21.69    -2.48
9540 PRO   ( 191-)  W  -   N    -10.0   -35.28    -2.48
9885 ILE   ( 137-)  Y  -   CA   -15.9     9.22    33.24
1134  PRO  ( 114-) B  -    N     -8.2   -29.44    -2.48
1216  PRO  (  18-) D  -    N      7.4    21.75    -2.48
1279  PRO  ( 191-) E  -    N    -14.8   -51.07    -2.48
1289  ALA  (   1-) F  -    CA   -17.5    11.91    34.09
The average deviation= 0.480

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.

9885 ILE   ( 137-)  Y  -  11.43
 155 LEU   ( 178-)  A  -   9.45
3120 ALA   (   1-)  H  -   8.78
1289  ALA  (   1-) F  -   8.76
3412 LEU   ( 178-)  I  -   8.20
7385 GLN   ( 408-)  R  -   7.63
3410 THR   ( 176-)  I  -   7.56
8086 ALA   ( 112-)  T  -   7.40
4829 ALA   ( 112-)  L  -   6.40
1064  GLN  ( 408-) Z  -   6.35
 871 GLN   ( 408-)  B  -   6.35
4128 GLN   ( 408-)  J  -   6.34
3372 GLU   ( 138-)  I  -   6.10
1125  ALA  (  21-) B  -   6.08
7995 ALA   (  21-)  T  -   6.06
1572 ALA   ( 112-)  D  -   5.21
7958 ASP   ( 494-)  S  -   4.97
1892 GLU   ( 432-)  D  -   4.68
9925 ALA   ( 177-)  Y  -   4.66
1166  GLU  ( 432-) B  -   4.64
1116  ALA  ( 442-) A  -   4.63
1392 ALA   ( 442-)  C  -   4.61
7906 ALA   ( 442-)  S  -   4.59
7907 GLN   ( 443-)  S  -   4.59
8406 GLU   ( 432-)  T  -   4.58
And so on for a total of 55 lines.

Error: Side chain planarity problems

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

3372 GLU   ( 138-)  I  -   4.61

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.447

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.

8257 THR   ( 283-)  T  -   -3.2
5000 THR   ( 283-)  L  -   -3.2
1743 THR   ( 283-)  D  -   -3.2
1151  THR  ( 283-) B  -   -3.2
 577 PRO   ( 114-)  B  -   -3.0
3834 PRO   ( 114-)  J  -   -3.0
1034  PRO  ( 114-) Z  -   -3.0
7091 PRO   ( 114-)  R  -   -3.0
9538 PRO   ( 189-)  W  -   -3.0
6628 ILE   ( 137-)  Q  -   -2.9
5458 THR   ( 283-)  M  -   -2.9
5521 PRO   ( 346-)  M  -   -2.9
1102  TYR  ( 308-) A  -   -2.9
4515 TYR   ( 308-)  K  -   -2.9
7772 TYR   ( 308-)  S  -   -2.9
1258 TYR   ( 308-)  C  -   -2.9
2201 THR   ( 283-)  E  -   -2.9
6283 PRO   ( 191-)  O  -   -2.9
5965 PRO   ( 332-)  N  -   -2.9
1279  PRO  ( 189-) E  -   -2.9
3026 PRO   ( 191-)  G  -   -2.9
5650 PHE   (  17-)  N  -   -2.9
1216  PHE  (  17-) D  -   -2.9
2393 PHE   (  17-)  F  -   -2.9
8907 PHE   (  17-)  V  -   -2.9
And so on for a total of 730 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 ASN   (  27-)  A  - Poor phi/psi
  13 ASP   (  36-)  A  - Poor phi/psi
  21 LEU   (  44-)  A  - Poor phi/psi
  35 ASN   (  58-)  A  - Poor phi/psi
  62 GLY   (  85-)  A  - Poor phi/psi
  67 CYS   (  90-)  A  - omega poor
  72 LEU   (  95-)  A  - Poor phi/psi
 112 GLY   ( 135-)  A  - omega poor
 114 ILE   ( 137-)  A  - omega poor
 115 GLU   ( 138-)  A  - omega poor
 120 ASP   ( 143-)  A  - Poor phi/psi
 150 THR   ( 173-)  A  - Poor phi/psi
 239 ASP   ( 262-)  A  - Poor phi/psi
 255 ARG   ( 278-)  A  - Poor phi/psi
 262 ALA   ( 285-)  A  - Poor phi/psi
 279 ALA   ( 302-)  A  - Poor phi/psi
 291 LYS   ( 314-)  A  - Poor phi/psi
 293 GLU   ( 316-)  A  - Poor phi/psi
 311 ALA   ( 334-)  A  - Poor phi/psi
 341 ILE   ( 364-)  A  - omega poor
 343 PRO   ( 366-)  A  - omega poor
 344 ALA   ( 367-)  A  - Poor phi/psi
 348 GLY   ( 371-)  A  - Poor phi/psi
 356 GLY   ( 379-)  A  - Poor phi/psi
 368 GLY   ( 391-)  A  - Poor phi/psi
And so on for a total of 773 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 : -5.180

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.

 443 SER   ( 466-)  A  -   0.36
3700 SER   ( 466-)  I  -   0.36
6957 SER   ( 466-)  Q  -   0.36
8368 ARG   ( 394-)  T  -   0.36
1021  SER  ( 466-) Y  -   0.36
1715 SER   ( 255-)  D  -   0.36
4972 SER   ( 255-)  L  -   0.36
8229 SER   ( 255-)  T  -   0.36
1148  SER  ( 255-) B  -   0.36
 710 GLU   ( 247-)  B  -   0.36
 737 SER   ( 274-)  B  -   0.36
1249 GLU   ( 299-)  C  -   0.36
3967 GLU   ( 247-)  J  -   0.36
3994 SER   ( 274-)  J  -   0.36
4506 GLU   ( 299-)  K  -   0.36
6083 GLU   ( 450-)  N  -   0.36
7224 GLU   ( 247-)  R  -   0.36
7251 SER   ( 274-)  R  -   0.36
7763 GLU   ( 299-)  S  -   0.36
1048  GLU  ( 247-) Z  -   0.36
1050  SER  ( 274-) Z  -   0.36
1102  GLU  ( 299-) A  -   0.36
3106 SER   ( 271-)  G  -   0.37
6363 SER   ( 271-)  O  -   0.37
9620 SER   ( 271-)  W  -   0.37
1287  SER  ( 271-) E  -   0.37
1822 SER   ( 362-)  D  -   0.37
2173 SER   ( 255-)  E  -   0.37
5430 SER   ( 255-)  M  -   0.37
8687 SER   ( 255-)  U  -   0.37
1194  SER  ( 255-) C  -   0.37
2622 ARG   ( 246-)  F  -   0.38
5879 ARG   ( 246-)  N  -   0.38
9136 ARG   ( 246-)  V  -   0.38
1239  ARG  ( 246-) D  -   0.38
8336 SER   ( 362-)  T  -   0.38
1224 SER   ( 274-)  C  -   0.38
4481 SER   ( 274-)  K  -   0.38
7738 SER   ( 274-)  S  -   0.38
1099  SER  ( 274-) A  -   0.38
1250  SER  ( 362-) D  -   0.38
ERROR. Too many residues to use DSSP

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 HIS   (  26-)  A  -     0
   4 ASN   (  27-)  A  -     0
   5 GLU   (  28-)  A  -     0
  12 SER   (  35-)  A  -     0
  13 ASP   (  36-)  A  -     0
  19 HIS   (  42-)  A  -     0
  21 LEU   (  44-)  A  -     0
  25 MET   (  48-)  A  -     0
  26 GLN   (  49-)  A  -     0
  33 PRO   (  56-)  A  -     0
  35 ASN   (  58-)  A  -     0
  36 ARG   (  59-)  A  -     0
  41 LEU   (  64-)  A  -     0
  45 ARG   (  68-)  A  -     0
  46 ASP   (  69-)  A  -     0
  53 MET   (  76-)  A  -     0
  55 PRO   (  78-)  A  -     0
  56 TYR   (  79-)  A  -     0
  61 GLU   (  84-)  A  -     0
  63 MET   (  86-)  A  -     0
  72 LEU   (  95-)  A  -     0
  73 GLU   (  96-)  A  -     0
  76 VAL   (  99-)  A  -     0
  78 ARG   ( 101-)  A  -     0
  81 LEU   ( 104-)  A  -     0
And so on for a total of 4620 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1508 GLY   (  48-)  D  -  3.16   16
1127  GLY  (  48-) B  -  3.16   16
4765 GLY   (  48-)  L  -  3.16   16
8022 GLY   (  48-)  T  -  3.16   16
8865 GLY   ( 433-)  U  -  2.33   11
5608 GLY   ( 433-)  M  -  2.24   11
1300  GLY  ( 110-) F  -  2.05   12
3229 GLY   ( 110-)  H  -  2.05   12
6486 GLY   ( 110-)  P  -  2.05   12
9743 GLY   ( 110-)  X  -  2.05   12
 953 GLY   ( 490-)  B  -  1.59   12
4210 GLY   ( 490-)  J  -  1.59   12
7467 GLY   ( 490-)  R  -  1.59   12
1072  GLY  ( 490-) Z  -  1.59   12
9938 GLY   ( 190-)  Y  -  1.58   11
6681 GLY   ( 190-)  Q  -  1.58   11
 167 GLY   ( 190-)  A  -  1.58   11
3424 GLY   ( 190-)  I  -  1.58   11
2518 GLY   ( 142-)  F  -  1.55   80
1228  GLY  ( 142-) D  -  1.55   80
5775 GLY   ( 142-)  N  -  1.55   80
9032 GLY   ( 142-)  V  -  1.55   80
1132  GLY  (  92-) B  -  1.54   12
1552 GLY   (  92-)  D  -  1.54   12
4809 GLY   (  92-)  L  -  1.54   12
8066 GLY   (  92-)  T  -  1.54   12
1006  GLY  ( 319-) Y  -  1.52   22
6810 GLY   ( 319-)  Q  -  1.52   22
 296 GLY   ( 319-)  A  -  1.52   22
3553 GLY   ( 319-)  I  -  1.52   22

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].

 561 PRO   (  98-)  B  - -132.0 half-chair C-delta/C-gamma (-126 degrees)
 577 PRO   ( 114-)  B  -  127.5 half-chair C-beta/C-alpha (126 degrees)
 608 PRO   ( 145-)  B  -  -19.6 half-chair C-alpha/N (-18 degrees)
2032 PRO   ( 114-)  E  - -113.5 envelop C-gamma (-108 degrees)
2264 PRO   ( 346-)  E  -  -17.6 half-chair C-alpha/N (-18 degrees)
2321 PRO   ( 403-)  E  -  -15.8 half-chair C-alpha/N (-18 degrees)
2394 PRO   (  18-)  F  -  159.2 half-chair C-alpha/N (162 degrees)
2490 PRO   ( 114-)  F  -   99.0 envelop C-beta (108 degrees)
2514 PRO   ( 138-)  F  -  -24.6 half-chair C-alpha/N (-18 degrees)
2722 PRO   ( 346-)  F  - -116.3 envelop C-gamma (-108 degrees)
3024 PRO   ( 189-)  G  -  102.5 envelop C-beta (108 degrees)
3026 PRO   ( 191-)  G  -  -63.2 envelop C-beta (-72 degrees)
3192 PRO   (  73-)  H  -  100.0 envelop C-beta (108 degrees)
3818 PRO   (  98-)  J  - -132.0 half-chair C-delta/C-gamma (-126 degrees)
3834 PRO   ( 114-)  J  -  127.6 half-chair C-beta/C-alpha (126 degrees)
3865 PRO   ( 145-)  J  -  -19.6 half-chair C-alpha/N (-18 degrees)
5289 PRO   ( 114-)  M  - -113.5 envelop C-gamma (-108 degrees)
5521 PRO   ( 346-)  M  -  -11.7 half-chair C-alpha/N (-18 degrees)
5578 PRO   ( 403-)  M  -  -13.7 half-chair C-alpha/N (-18 degrees)
5651 PRO   (  18-)  N  -  159.2 half-chair C-alpha/N (162 degrees)
5771 PRO   ( 138-)  N  -  -24.6 half-chair C-alpha/N (-18 degrees)
5979 PRO   ( 346-)  N  - -115.3 envelop C-gamma (-108 degrees)
6283 PRO   ( 191-)  O  - -115.5 envelop C-gamma (-108 degrees)
6449 PRO   (  73-)  P  -  100.1 envelop C-beta (108 degrees)
7075 PRO   (  98-)  R  - -132.0 half-chair C-delta/C-gamma (-126 degrees)
7091 PRO   ( 114-)  R  -  127.6 half-chair C-beta/C-alpha (126 degrees)
7122 PRO   ( 145-)  R  -  -19.6 half-chair C-alpha/N (-18 degrees)
8546 PRO   ( 114-)  U  - -113.5 envelop C-gamma (-108 degrees)
8778 PRO   ( 346-)  U  -   -1.5 envelop N (0 degrees)
8835 PRO   ( 403-)  U  -  -13.4 half-chair C-alpha/N (-18 degrees)
8908 PRO   (  18-)  V  -  159.2 half-chair C-alpha/N (162 degrees)
9028 PRO   ( 138-)  V  -  -24.6 half-chair C-alpha/N (-18 degrees)
9236 PRO   ( 346-)  V  - -112.1 envelop C-gamma (-108 degrees)
9538 PRO   ( 189-)  W  -  -45.8 half-chair C-beta/C-alpha (-54 degrees)
9706 PRO   (  73-)  X  -  100.0 envelop C-beta (108 degrees)
1033  PRO  (  98-) Z  - -132.0 half-chair C-delta/C-gamma (-126 degrees)
1034  PRO  ( 114-) Z  -  127.5 half-chair C-beta/C-alpha (126 degrees)
1037  PRO  ( 145-) Z  -  -19.6 half-chair C-alpha/N (-18 degrees)
1134  PRO  ( 114-) B  - -113.4 envelop C-gamma (-108 degrees)
1180  PRO  ( 114-) C  - -113.5 envelop C-gamma (-108 degrees)
1203  PRO  ( 346-) C  -   -0.7 envelop N (0 degrees)
1209  PRO  ( 403-) C  -  -17.1 half-chair C-alpha/N (-18 degrees)
1216  PRO  (  18-) D  -  159.2 half-chair C-alpha/N (162 degrees)
1226  PRO  ( 114-) D  -   99.0 envelop C-beta (108 degrees)
1228  PRO  ( 138-) D  -  -24.6 half-chair C-alpha/N (-18 degrees)
1249  PRO  ( 346-) D  - -116.0 envelop C-gamma (-108 degrees)
1279  PRO  ( 191-) E  -  154.7 half-chair C-alpha/N (162 degrees)
1296  PRO  (  73-) F  -  100.0 envelop C-beta (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.

7027 GLY   (  50-)  R  -   O   <-> 7071 ILE   (  94-)  R  -   CG2    1.17    1.63  INTRA BF
7027 GLY   (  50-)  R  -   C   <-> 7071 ILE   (  94-)  R  -   CG2    1.15    2.05  INTRA BF
7072 LEU   (  95-)  R  -   CD2 <-> 7106 VAL   ( 129-)  R  -   CG2    1.02    2.18  INTRA BF
7028 GLU   (  51-)  R  -   CA  <-> 7071 ILE   (  94-)  R  -   CG2    0.94    2.26  INTRA BF
1279  LEU  ( 190-) E  -    CD1 <-> 1279  PRO  ( 191-) E  -    N      0.89    2.11  INTRA BF
9535 GLN   ( 186-)  W  -   NE2 <-> 9538 PRO   ( 189-)  W  -   CG     0.86    2.24  INTRA BF
3414 ILE   ( 180-)  I  -   CD1 <-> 3445 LYS   ( 211-)  I  -   NZ     0.83    2.27  INTRA BF
2264 PRO   ( 346-)  E  -   CG  <-> 2266 VAL   ( 348-)  E  -   CG1    0.81    2.39  INTRA BF
 114 ILE   ( 137-)  A  -   CD1 <->  115 GLU   ( 138-)  A  -   CA     0.80    2.30  INTRA BF
9536 LEU   ( 187-)  W  -   CD1 <-> 9537 LEU   ( 188-)  W  -   CB     0.80    2.30  INTRA BL
2262 LEU   ( 344-)  E  -   C   <-> 2264 PRO   ( 346-)  E  -   CD     0.80    2.40  INTRA BF
7028 GLU   (  51-)  R  -   N   <-> 7071 ILE   (  94-)  R  -   CG2    0.79    2.31  INTRA BF
6378 MET   (   2-)  P  -   CE  <-> 1188  ASN  ( 197-) C  -    CB     0.78    2.42  INTRA BF
 114 ILE   ( 137-)  A  -   CD1 <->  115 GLU   ( 138-)  A  -   CB     0.78    2.32  INTRA BF
9539 LEU   ( 190-)  W  -   CD1 <-> 9540 PRO   ( 191-)  W  -   N      0.77    2.23  INTRA BF
7956 TYR   ( 492-)  S  -   O   <-> 7957 ASN   ( 493-)  S  -   ND2    0.72    1.88  INTRA BF
1134  ALA  ( 113-) B  -    CB  <-> 1151  ARG  ( 281-) B  -    CG     0.72    2.48  INTRA BF
1134  ALA  ( 113-) B  -    CB  <-> 1134  PRO  ( 114-) B  -    CD     0.72    2.38  INTRA BF
 114 ILE   ( 137-)  A  -   CD1 <->  115 GLU   ( 138-)  A  -   N      0.70    2.30  INTRA BF
1134  ARG  ( 111-) B  -    CD  <-> 1134  ALA  ( 112-) B  -    N      0.70    2.30  INTRA BF
 115 GLU   ( 138-)  A  -   CG  <->  282 ASN   ( 305-)  A  -   CG     0.69    2.51  INTRA BF
1134  ARG  ( 111-) B  -    CG  <-> 1134  ALA  ( 112-) B  -    N      0.69    2.31  INTRA BF
2265 LEU   ( 347-)  E  -   C   <-> 2266 VAL   ( 348-)  E  -   CG1    0.69    2.41  INTRA BF
4343 VAL   ( 136-)  K  -   C   <-> 4344 ILE   ( 137-)  K  -   CG1    0.68    2.42  INTRA BF
3817 VAL   (  97-)  J  -   CG1 <-> 3818 PRO   (  98-)  J  -   CD     0.67    2.53  INTRA BL
And so on for a total of 2476 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

4129 PHE   ( 409-)  J  -     -8.13
7386 PHE   ( 409-)  R  -     -8.13
1064  PHE  ( 409-) Z  -     -8.13
 872 PHE   ( 409-)  B  -     -8.13
5048 TYR   ( 331-)  L  -     -7.91
1262 PHE   ( 312-)  C  -     -7.88
1103  PHE  ( 312-) A  -     -7.88
4519 PHE   ( 312-)  K  -     -7.88
7776 PHE   ( 312-)  S  -     -7.88
1791 TYR   ( 331-)  D  -     -7.88
8305 TYR   ( 331-)  T  -     -7.86
1156  TYR  ( 331-) B  -     -7.77
1247  TYR  ( 331-) D  -     -7.70
9221 TYR   ( 331-)  V  -     -7.66
2707 TYR   ( 331-)  F  -     -7.61
9411 TYR   (  62-)  W  -     -7.50
1266  TYR  (  62-) E  -     -7.48
1134  ARG  ( 111-) B  -     -7.46
2897 TYR   (  62-)  G  -     -7.46
6154 TYR   (  62-)  O  -     -7.46
5964 TYR   ( 331-)  N  -     -7.45
2249 TYR   ( 331-)  E  -     -7.18
8763 TYR   ( 331-)  U  -     -7.16
8987 MET   (  97-)  V  -     -7.15
 256 ARG   ( 279-)  A  -     -7.08
And so on for a total of 476 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.

 191 GLU   ( 214-)  A  -    193 - GLY    216- ( A)  -      -5.11
 255 ARG   ( 278-)  A  -    257 - PRO    280- ( A)  -      -5.68
 650 ARG   ( 187-)  B  -    652 - SER    189- ( B)  -      -4.54
 741 ARG   ( 278-)  B  -    743 - PRO    280- ( B)  -      -5.52
2897 TYR   (  62-)  G  -   2899 - HIS     64- ( G)  -      -5.96
3033 LEU   ( 198-)  G  -   3035 - HIS    200- ( G)  -      -5.49
3448 GLU   ( 214-)  I  -   3450 - GLY    216- ( I)  -      -5.11
3512 ARG   ( 278-)  I  -   3514 - PRO    280- ( I)  -      -5.72
3907 ARG   ( 187-)  J  -   3909 - SER    189- ( J)  -      -4.54
3998 ARG   ( 278-)  J  -   4000 - PRO    280- ( J)  -      -5.53
6154 TYR   (  62-)  O  -   6156 - HIS     64- ( O)  -      -5.97
6290 LEU   ( 198-)  O  -   6292 - HIS    200- ( O)  -      -5.49
6627 VAL   ( 136-)  Q  -   6629 - GLU    138- ( Q)  -      -4.41
6705 GLU   ( 214-)  Q  -   6707 - GLY    216- ( Q)  -      -5.11
6769 ARG   ( 278-)  Q  -   6771 - PRO    280- ( Q)  -      -5.75
7164 ARG   ( 187-)  R  -   7166 - SER    189- ( R)  -      -4.54
7255 ARG   ( 278-)  R  -   7257 - PRO    280- ( R)  -      -5.55
9411 TYR   (  62-)  W  -   9413 - HIS     64- ( W)  -      -5.99
9547 LEU   ( 198-)  W  -   9549 - HIS    200- ( W)  -      -5.49
9962 GLU   ( 214-)  Y  -   9964 - GLY    216- ( Y)  -      -5.10
1002  ARG  ( 278-) Y  -    1002 -  PRO   280- (Y ) -       -5.80
1042  ARG  ( 187-) Z  -    1042 -  SER   189- (Z ) -       -4.54
1099  ARG  ( 278-) A  -    1100 -  PRO   280- (A ) -       -5.37
1134  HIS  ( 110-) B  -    1134 -  ALA   112- (B ) -       -5.40
1134  SER  ( 115-) B  -    1134 -  GLU   117- (B ) -       -4.73
1266  TYR  (  62-) E  -    1267 -  HIS    64- (E ) -       -5.98
1280  LEU  ( 198-) E  -    1280 -  HIS   200- (E ) -       -5.49

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

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: F

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

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

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: L

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: M

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: N

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: O

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: P

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: Q

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: R

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: S

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: T

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: U

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: V

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: W

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: X

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: Y

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: Z

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

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: F

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.

1089  GLN  ( 172-) A  -  -3.25
1115  GLN  ( 435-) A  -  -3.18
2895 LEU   (  60-)  G  -  -3.16
6152 LEU   (  60-)  O  -  -3.16
1266  LEU  (  60-) E  -  -3.16
7899 GLN   ( 435-)  S  -  -3.11
1385 GLN   ( 435-)  C  -  -3.10
6293 LYS   ( 201-)  O  -  -3.03
3036 LYS   ( 201-)  G  -  -2.94
3669 GLN   ( 435-)  I  -  -2.90
 911 LEU   ( 448-)  B  -  -2.88
7425 LEU   ( 448-)  R  -  -2.88
1068  LEU  ( 448-) Z  -  -2.87
4168 LEU   ( 448-)  J  -  -2.87
3682 LEU   ( 448-)  I  -  -2.87
6939 LEU   ( 448-)  Q  -  -2.87
1019  LEU  ( 448-) Y  -  -2.87
 425 LEU   ( 448-)  A  -  -2.86
6926 GLN   ( 435-)  Q  -  -2.85
9488 MET   ( 139-)  W  -  -2.84
6231 MET   ( 139-)  O  -  -2.84
2974 MET   ( 139-)  G  -  -2.83
8776 LEU   ( 344-)  U  -  -2.76
4655 LEU   ( 448-)  K  -  -2.75
7912 LEU   ( 448-)  S  -  -2.75
And so on for a total of 74 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.

 897 LYS   ( 434-)  B  -  -  900 ALA   ( 437-)  B  -     -1.70
 918 TYR   ( 455-)  B  -  -  921 ASP   ( 458-)  B  -     -2.10
1120 ASP   ( 170-)  C  -  - 1123 THR   ( 173-)  C  -     -1.56
1258 TYR   ( 308-)  C  -  - 1261 ALA   ( 311-)  C  -     -1.59
3663 GLU   ( 429-)  I  -  - 3666 LYS   ( 432-)  I  -     -1.76
4154 LYS   ( 434-)  J  -  - 4157 ALA   ( 437-)  J  -     -1.70
4175 TYR   ( 455-)  J  -  - 4178 ASP   ( 458-)  J  -     -2.10
4377 ASP   ( 170-)  K  -  - 4380 THR   ( 173-)  K  -     -1.55
4515 TYR   ( 308-)  K  -  - 4518 ALA   ( 311-)  K  -     -1.59
7411 LYS   ( 434-)  R  -  - 7414 ALA   ( 437-)  R  -     -1.70
7432 TYR   ( 455-)  R  -  - 7435 ASP   ( 458-)  R  -     -2.04
7634 ASP   ( 170-)  S  -  - 7637 THR   ( 173-)  S  -     -1.55
1068  TYR  ( 455-) Z  -   - 1069  ASP  ( 458-) Z  -      -2.04
1089  ASP  ( 170-) A  -   - 1089  THR  ( 173-) A  -      -1.82
ERROR. Too many residues to use DSSP

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

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.

1307  HOH  ( 515 ) B  -    O
1308  HOH  ( 514 ) C  -    O
1308  HOH  ( 460 ) D  -    O
1308  HOH  ( 462 ) D  -    O
1308  HOH  ( 467 ) D  -    O
1308  HOH  ( 463 ) F  -    O
1308  HOH  ( 289 ) G  -    O
1308  HOH  ( 294 ) G  -    O
1308  HOH  ( 460 ) L  -    O
1308  HOH  ( 465 ) L  -    O
1308  HOH  ( 460 ) N  -    O
1308  HOH  ( 288 ) O  -    O
1308  HOH  ( 290 ) O  -    O
1309  HOH  ( 514 ) S  -    O
1309  HOH  ( 460 ) V  -    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.

  26 GLN   (  49-)  A  -
  86 ASN   ( 109-)  A  -
 149 GLN   ( 172-)  A  -
 162 ASN   ( 185-)  A  -
 163 GLN   ( 186-)  A  -
 359 GLN   ( 382-)  A  -
 385 GLN   ( 408-)  A  -
 512 GLN   (  49-)  B  -
 607 GLN   ( 144-)  B  -
 648 ASN   ( 185-)  B  -
 649 GLN   ( 186-)  B  -
 729 GLN   ( 266-)  B  -
 862 GLN   ( 399-)  B  -
 886 HIS   ( 423-)  B  -
 906 GLN   ( 443-)  B  -
 950 ASN   ( 487-)  B  -
 976 HIS   (  26-)  C  -
1135 ASN   ( 185-)  C  -
1136 GLN   ( 186-)  C  -
1216 GLN   ( 266-)  C  -
1332 GLN   ( 382-)  C  -
1437 ASN   ( 487-)  C  -
1467 GLN   (   7-)  D  -
1479 GLN   (  19-)  D  -
1503 GLN   (  43-)  D  -
And so on for a total of 168 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.

   4 ASN   (  27-)  A  -   N
  13 ASP   (  36-)  A  -   N
  14 GLY   (  37-)  A  -   N
  23 ASP   (  46-)  A  -   N
  26 GLN   (  49-)  A  -   NE2
  47 SER   (  70-)  A  -   N
  54 GLY   (  77-)  A  -   N
  57 ALA   (  80-)  A  -   N
  59 LEU   (  82-)  A  -   N
  68 THR   (  91-)  A  -   N
  72 LEU   (  95-)  A  -   N
  78 ARG   ( 101-)  A  -   NE
  83 ARG   ( 106-)  A  -   NE
  83 ARG   ( 106-)  A  -   NH2
  88 LEU   ( 111-)  A  -   N
  94 GLY   ( 117-)  A  -   N
  95 LYS   ( 118-)  A  -   N
  99 ASP   ( 122-)  A  -   N
 108 ALA   ( 131-)  A  -   N
 114 ILE   ( 137-)  A  -   N
 116 ARG   ( 139-)  A  -   N
 117 GLN   ( 140-)  A  -   N
 120 ASP   ( 143-)  A  -   N
 121 GLN   ( 144-)  A  -   N
 125 THR   ( 148-)  A  -   OG1
And so on for a total of 2037 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.

  28 GLU   (  51-)  A  -   OE2
 142 GLU   ( 165-)  A  -   OE1
 142 GLU   ( 165-)  A  -   OE2
 192 HIS   ( 215-)  A  -   ND1
 231 GLU   ( 254-)  A  -   OE1
 238 ASP   ( 261-)  A  -   OD1
 243 GLN   ( 266-)  A  -   OE1
 335 ASN   ( 358-)  A  -   OD1
 420 GLN   ( 443-)  A  -   OE1
 453 ASP   ( 476-)  A  -   OD1
 474 GLU   ( 497-)  A  -   OE1
 514 GLU   (  51-)  B  -   OE2
 601 GLU   ( 138-)  B  -   OE2
 628 GLU   ( 165-)  B  -   OE1
 628 GLU   ( 165-)  B  -   OE2
 644 ASP   ( 181-)  B  -   OD1
 693 GLU   ( 230-)  B  -   OE1
 710 GLU   ( 247-)  B  -   OE2
 717 GLU   ( 254-)  B  -   OE1
 815 GLN   ( 352-)  B  -   OE1
 886 HIS   ( 423-)  B  -   ND1
 923 GLU   ( 460-)  B  -   OE1
 923 GLU   ( 460-)  B  -   OE2
1115 GLU   ( 165-)  C  -   OE1
1239 ASP   ( 289-)  C  -   OD1
And so on for a total of 244 lines.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1303   MG  ( 601-) A  -  -.-  -.-  Too few ligands (3)
1303   MG  ( 601-) B  -  -.-  -.-  Low probability ion. B=125.5
1303   MG  ( 601-) C  -  -.-  -.-  Too few ligands (3)
1303   MG  ( 601-) D  -    0.62   1.06 Scores about as good as CA
1304   MG  ( 601-) I  -  -.-  -.-  Too few ligands (3)
1304   MG  ( 601-) J  -  -.-  -.-  Low probability ion. B=122.7
1304   MG  ( 601-) K  -  -.-  -.-  Too few ligands (3)
1304   MG  ( 601-) L  -    0.66   1.16 Scores about as good as CA
1305   MG  ( 601-) Q  -  -.-  -.-  Too few ligands (3)
1305   MG  ( 601-) R  -  -.-  -.-  Low probability ion. B=118.2
1305   MG  ( 601-) S  -  -.-  -.-  Too few ligands (3)
1306   MG  ( 601-) T  -  -.-  -.-  Low probability ion. B= 80.3
1306   MG  ( 601-) Z  -  -.-  -.-  Low probability ion. B=147.2
1307   MG  ( 601-) A  -  -.-  -.-  Low probability ion. B= 83.0
1307   MG  ( 601-) B  -  -.-  -.-  Low probability ion. B=127.4

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.

  28 GLU   (  51-)  A  -  H-bonding suggests Gln
  46 ASP   (  69-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
  61 GLU   (  84-)  A  -  H-bonding suggests Gln
 142 GLU   ( 165-)  A  -  H-bonding suggests Gln
 158 ASP   ( 181-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 190 GLU   ( 213-)  A  -  H-bonding suggests Gln; but Alt-Rotamer
 228 ASP   ( 251-)  A  -  H-bonding suggests Asn
 482 ASP   ( 505-)  A  -  H-bonding suggests Asn
 514 GLU   (  51-)  B  -  H-bonding suggests Gln
 579 ASP   ( 116-)  B  -  H-bonding suggests Asn
 628 GLU   ( 165-)  B  -  H-bonding suggests Gln
 644 ASP   ( 181-)  B  -  H-bonding suggests Asn
 714 ASP   ( 251-)  B  -  H-bonding suggests Asn
 779 GLU   ( 316-)  B  -  H-bonding suggests Gln
 813 ASP   ( 350-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 865 GLU   ( 402-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
 915 GLU   ( 452-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
 921 ASP   ( 458-)  B  -  H-bonding suggests Asn
 923 GLU   ( 460-)  B  -  H-bonding suggests Gln
 939 ASP   ( 476-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
 968 ASP   ( 505-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
1001 GLU   (  51-)  C  -  H-bonding suggests Gln
1019 ASP   (  69-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
1115 GLU   ( 165-)  C  -  H-bonding suggests Gln
1120 ASP   ( 170-)  C  -  H-bonding suggests Asn; but Alt-Rotamer
And so on for a total of 247 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 :  -1.458
  2nd generation packing quality :  -2.535
  Ramachandran plot appearance   :  -3.447 (poor)
  chi-1/chi-2 rotamer normality  :  -5.180 (bad)
  Backbone conformation          :  -0.494

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.198 (tight)
  Bond angles                    :   0.454 (tight)
  Omega angle restraints         :   1.016
  Side chain planarity           :   0.190 (tight)
  Improper dihedral distribution :   0.517
  B-factor distribution          :   0.773
  Inside/Outside distribution    :   1.034

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 3.26


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.198 (tight)
  Bond angles                    :   0.454 (tight)
  Omega angle restraints         :   1.016
  Side chain planarity           :   0.190 (tight)
  Improper dihedral distribution :   0.517
  B-factor distribution          :   0.773
  Inside/Outside distribution    :   1.034
==============

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.