WHAT IF Check report

This file was created 2012-01-13 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 pdb1uzd.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.087
CA-only RMS fit for the two chains : 0.052

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.112
CA-only RMS fit for the two chains : 0.051

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 H

All-atom RMS fit for the two chains : 0.142
CA-only RMS fit for the two chains : 0.050

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and K

All-atom RMS fit for the two chains : 0.081
CA-only RMS fit for the two chains : 0.046

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

4785 CAP   (1477-)  A  -
4792 CAP   (1477-)  B  -
4801 CAP   (1477-)  E  -
4809 CAP   (1477-)  H  -
4817 CAP   (1477-)  K  -
4825 CAP   (1477-)  O  -
4834 CAP   (1477-)  R  -
4853 CAP   (1477-)  V  -

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: E

Note: Ramachandran plot

Chain identifier: F

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: M

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

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

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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: M

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

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.

 177 ARG   ( 187-)  A
 644 ARG   ( 187-)  B
1238 ARG   ( 187-)  E
1836 ARG   ( 187-)  H
2563 ARG   ( 187-)  K
3161 ARG   ( 187-)  O
3755 ARG   ( 187-)  R
4350 ARG   ( 187-)  V

Warning: Tyrosine convention problem

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

1030 TYR   (  98-)  C
1154 TYR   ( 103-)  E
1624 TYR   (  98-)  F
2222 TYR   (  98-)  I
2351 TYR   (  98-)  J
2479 TYR   ( 103-)  K
2949 TYR   (  98-)  M
3547 TYR   (  98-)  P
3653 TYR   (  85-)  R
4141 TYR   (  98-)  T

Warning: Phenylalanine convention problem

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

 392 PHE   ( 402-)  A
 859 PHE   ( 402-)  B
 944 PHE   (  12-)  C
 947 PHE   (  15-)  C
 976 PHE   (  44-)  C
1026 PHE   (  94-)  C
1453 PHE   ( 402-)  E
1520 PHE   ( 469-)  E
1538 PHE   (  12-)  F
1541 PHE   (  15-)  F
1570 PHE   (  44-)  F
1620 PHE   (  94-)  F
2051 PHE   ( 402-)  H
2118 PHE   ( 469-)  H
2136 PHE   (  12-)  I
2139 PHE   (  15-)  I
2168 PHE   (  44-)  I
2218 PHE   (  94-)  I
2265 PHE   (  12-)  J
2268 PHE   (  15-)  J
2297 PHE   (  44-)  J
2347 PHE   (  94-)  J
2778 PHE   ( 402-)  K
2845 PHE   ( 469-)  K
2863 PHE   (  12-)  M
2866 PHE   (  15-)  M
2895 PHE   (  44-)  M
2945 PHE   (  94-)  M
3376 PHE   ( 402-)  O
3443 PHE   ( 469-)  O
3461 PHE   (  12-)  P
3464 PHE   (  15-)  P
3493 PHE   (  44-)  P
3543 PHE   (  94-)  P
3970 PHE   ( 402-)  R
4055 PHE   (  12-)  T
4058 PHE   (  15-)  T
4087 PHE   (  44-)  T
4137 PHE   (  94-)  T
4565 PHE   ( 402-)  V
4632 PHE   ( 469-)  V
4650 PHE   (  12-)  W
4653 PHE   (  15-)  W
4682 PHE   (  44-)  W
4732 PHE   (  94-)  W

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.

  78 GLU   (  88-)  A
 326 GLU   ( 336-)  A
 450 GLU   ( 460-)  A
 545 GLU   (  88-)  B
 793 GLU   ( 336-)  B
 917 GLU   ( 460-)  B
1102 GLU   (  51-)  E
1139 GLU   (  88-)  E
1511 GLU   ( 460-)  E
1737 GLU   (  88-)  H
2109 GLU   ( 460-)  H
2464 GLU   (  88-)  K
2836 GLU   ( 460-)  K
3062 GLU   (  88-)  O
3310 GLU   ( 336-)  O
3434 GLU   ( 460-)  O
3656 GLU   (  88-)  R
4028 GLU   ( 460-)  R
4251 GLU   (  88-)  V
4623 GLU   ( 460-)  V

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 191 KCX   ( 201-)  A      CH     CX
 191 KCX   ( 201-)  A      OX1    OQ1
 191 KCX   ( 201-)  A      OX2    OQ2
 658 KCX   ( 201-)  B      CH     CX
 658 KCX   ( 201-)  B      OX1    OQ1
 658 KCX   ( 201-)  B      OX2    OQ2
1252 KCX   ( 201-)  E      CH     CX
1252 KCX   ( 201-)  E      OX1    OQ1
1252 KCX   ( 201-)  E      OX2    OQ2
1850 KCX   ( 201-)  H      CH     CX
1850 KCX   ( 201-)  H      OX1    OQ1
1850 KCX   ( 201-)  H      OX2    OQ2
2577 KCX   ( 201-)  K      CH     CX
2577 KCX   ( 201-)  K      OX1    OQ1
2577 KCX   ( 201-)  K      OX2    OQ2
3175 KCX   ( 201-)  O      CH     CX
3175 KCX   ( 201-)  O      OX1    OQ1
3175 KCX   ( 201-)  O      OX2    OQ2
3769 KCX   ( 201-)  R      CH     CX
3769 KCX   ( 201-)  R      OX1    OQ1
3769 KCX   ( 201-)  R      OX2    OQ2
4364 KCX   ( 201-)  V      CH     CX
4364 KCX   ( 201-)  V      OX1    OQ1
4364 KCX   ( 201-)  V      OX2    OQ2

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.

2383 THR   (   7-)  K      CA   CB    1.61    4.0

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

 |  0.997034  0.000115 -0.000009|
 |  0.000115  0.998585  0.000012|
 | -0.000009  0.000012  0.998104|
Proposed new scale matrix

 |  0.004559  0.000000  0.000000|
 |  0.000000  0.004469  0.000000|
 |  0.000000  0.000000  0.008967|
With corresponding cell

    A    = 219.369  B   = 223.747  C    = 111.520
    Alpha=  90.002  Beta=  90.002  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 220.014  B   = 224.078  C    = 111.725
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 728.861
(Under-)estimated Z-score: 19.897

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.

 288 HIS   ( 298-)  A      CG   ND1  CE1 109.88    4.3
 610 HIS   ( 153-)  B      CG   ND1  CE1 109.62    4.0
 724 HIS   ( 267-)  B      CG   ND1  CE1 109.74    4.1
 755 HIS   ( 298-)  B      CG   ND1  CE1 109.71    4.1
 934 MET   (   2-)  C      CB   CG   SD  125.06    4.1
 939 VAL   (   7-)  C      C    CA   CB  100.56   -5.0
 940 ASN   (   8-)  C      N    CA   C    94.56   -5.9
1434 HIS   ( 383-)  E      CG   ND1  CE1 109.68    4.1
1534 ASN   (   8-)  F     -C    N    CA  131.41    5.4
1581 HIS   (  55-)  F      CG   ND1  CE1 109.72    4.1
2260 VAL   (   7-)  J      C    CA   CB  100.65   -5.0
2261 ASN   (   8-)  J      N    CA   C    95.57   -5.6
2308 HIS   (  55-)  J      CG   ND1  CE1 109.70    4.1
2858 VAL   (   7-)  M      C    CA   CB  100.39   -5.1
2859 ASN   (   8-)  M      N    CA   C    94.32   -6.0
2997 THR   (  23-)  O      CG2  CB   OG1 101.15   -4.1
3092 THR   ( 118-)  O      CG2  CB   OG1 100.15   -4.6
3456 VAL   (   7-)  P      C    CA   CB  101.77   -4.4
3457 ASN   (   8-)  P      N    CA   C    95.98   -5.4
3504 HIS   (  55-)  P      CG   ND1  CE1 109.63    4.0
3806 HIS   ( 238-)  R      CG   ND1  CE1 109.63    4.0
4050 VAL   (   7-)  T      C    CA   CB  100.70   -4.9
4051 ASN   (   8-)  T     -C    N    CA  129.19    4.2
4051 ASN   (   8-)  T      N    CA   C    94.14   -6.1
4098 HIS   (  55-)  T      CG   ND1  CE1 109.75    4.1
4572 HIS   ( 409-)  V      CG   ND1  CE1 109.78    4.2
4645 VAL   (   7-)  W      C    CA   CB  101.12   -4.7
4646 ASN   (   8-)  W     -C    N    CA  129.48    4.3
4646 ASN   (   8-)  W      N    CA   C    95.35   -5.7

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.

  78 GLU   (  88-)  A
 177 ARG   ( 187-)  A
 326 GLU   ( 336-)  A
 450 GLU   ( 460-)  A
 545 GLU   (  88-)  B
 644 ARG   ( 187-)  B
 793 GLU   ( 336-)  B
 917 GLU   ( 460-)  B
1102 GLU   (  51-)  E
1139 GLU   (  88-)  E
1238 ARG   ( 187-)  E
1511 GLU   ( 460-)  E
1737 GLU   (  88-)  H
1836 ARG   ( 187-)  H
2109 GLU   ( 460-)  H
2464 GLU   (  88-)  K
2563 ARG   ( 187-)  K
2836 GLU   ( 460-)  K
3062 GLU   (  88-)  O
3161 ARG   ( 187-)  O
3310 GLU   ( 336-)  O
3434 GLU   ( 460-)  O
3656 GLU   (  88-)  R
3755 ARG   ( 187-)  R
4028 GLU   ( 460-)  R
4251 GLU   (  88-)  V
4350 ARG   ( 187-)  V
4623 GLU   ( 460-)  V

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.

 939 VAL   (   7-)  C      CA     6.2    42.22    33.23
4050 VAL   (   7-)  T      CA     6.1    42.11    33.23
The average deviation= 0.926

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.

4051 ASN   (   8-)  T    5.76
2859 ASN   (   8-)  M    5.70
 940 ASN   (   8-)  C    5.62
 292 ASP   ( 302-)  A    5.44
4646 ASN   (   8-)  W    5.36
3870 ASP   ( 302-)  R    5.33
2261 ASN   (   8-)  J    5.29
1951 ASP   ( 302-)  H    5.24
3457 ASN   (   8-)  P    5.15
2678 ASP   ( 302-)  K    5.15
3276 ASP   ( 302-)  O    4.50
 145 ILE   ( 155-)  A    4.36
4465 ASP   ( 302-)  V    4.31
1353 ASP   ( 302-)  E    4.20
 759 ASP   ( 302-)  B    4.01

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

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

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

2615 TYR   ( 239-)  K    -2.7
 229 TYR   ( 239-)  A    -2.7
3807 TYR   ( 239-)  R    -2.7
1290 TYR   ( 239-)  E    -2.6
3582 LYS   (  14-)  R    -2.5
3213 TYR   ( 239-)  O    -2.5
   4 LYS   (  14-)  A    -2.5
2390 LYS   (  14-)  K    -2.5
4177 LYS   (  14-)  V    -2.5
1663 LYS   (  14-)  H    -2.5
2988 LYS   (  14-)  O    -2.5
1065 LYS   (  14-)  E    -2.5
 471 LYS   (  14-)  B    -2.5
2640 ILE   ( 264-)  K    -2.4
4402 TYR   ( 239-)  V    -2.4
 696 TYR   ( 239-)  B    -2.4
2365 ILE   ( 112-)  J    -2.3
1638 ILE   ( 112-)  F    -2.3
3561 ILE   ( 112-)  P    -2.3
4750 ILE   ( 112-)  W    -2.3
4155 ILE   ( 112-)  T    -2.3
1044 ILE   ( 112-)  C    -2.3
2963 ILE   ( 112-)  M    -2.3
2236 ILE   ( 112-)  I    -2.3
 721 ILE   ( 264-)  B    -2.3
And so on for a total of 111 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.

  13 THR   (  23-)  A  omega poor
  31 ARG   (  41-)  A  omega poor
  52 SER   (  62-)  A  Poor phi/psi
  53 THR   (  63-)  A  Poor phi/psi
  71 LYS   (  81-)  A  omega poor
  97 LEU   ( 107-)  A  omega poor
 113 ASN   ( 123-)  A  omega poor
 153 ASN   ( 163-)  A  Poor phi/psi
 155 TYR   ( 165-)  A  omega poor
 165 LYS   ( 175-)  A  PRO omega poor
 189 PHE   ( 199-)  A  omega poor
 197 ASN   ( 207-)  A  Poor phi/psi
 253 PRO   ( 263-)  A  omega poor
 287 MET   ( 297-)  A  Poor phi/psi
 321 VAL   ( 331-)  A  Poor phi/psi
 340 ARG   ( 350-)  A  omega poor
 360 SER   ( 370-)  A  Poor phi/psi
 454 GLU   ( 464-)  A  omega poor
 480 THR   (  23-)  B  omega poor
 498 ARG   (  41-)  B  omega poor
 519 SER   (  62-)  B  Poor phi/psi
 520 THR   (  63-)  B  Poor phi/psi
 611 GLY   ( 154-)  B  omega poor
 620 ASN   ( 163-)  B  Poor phi/psi
 622 TYR   ( 165-)  B  omega poor
And so on for a total of 205 lines.

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.

4610 SER   ( 447-)  V    0.35
1928 SER   ( 279-)  H    0.35
1330 SER   ( 279-)  E    0.35
3421 SER   ( 447-)  O    0.36
 269 SER   ( 279-)  A    0.37
3847 SER   ( 279-)  R    0.37
 736 SER   ( 279-)  B    0.38
3253 SER   ( 279-)  O    0.39
2655 SER   ( 279-)  K    0.40

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   (  13-)  A      0
   5 ALA   (  15-)  A      0
   8 LYS   (  18-)  A      0
  13 THR   (  23-)  A      0
  14 TYR   (  24-)  A      0
  15 TYR   (  25-)  A      0
  16 THR   (  26-)  A      0
  19 TYR   (  29-)  A      0
  36 PRO   (  46-)  A      0
  51 SER   (  61-)  A      0
  52 SER   (  62-)  A      0
  53 THR   (  63-)  A      0
  56 TRP   (  66-)  A      0
  60 TRP   (  70-)  A      0
  64 LEU   (  74-)  A      0
  65 THR   (  75-)  A      0
  75 TYR   (  85-)  A      0
  76 ASP   (  86-)  A      0
  81 PRO   (  91-)  A      0
  83 GLU   (  93-)  A      0
  84 ASP   (  94-)  A      0
  85 ASN   (  95-)  A      0
  86 GLN   (  96-)  A      0
  94 HYP   ( 104-)  A      0
 100 GLU   ( 110-)  A      0
And so on for a total of 1816 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!

1986 GLY   ( 337-)  H   2.33   13
2713 GLY   ( 337-)  K   2.31   11
4500 GLY   ( 337-)  V   2.29   14
 327 GLY   ( 337-)  A   2.29   11
3905 GLY   ( 337-)  R   2.24   10
1388 GLY   ( 337-)  E   2.23   10
3311 GLY   ( 337-)  O   2.19   13
 794 GLY   ( 337-)  B   2.19   10

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...

4057 THR   (  14-)  T   1.52

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]

 507 PRO   (  50-)  B    0.20 LOW
 546 PRO   (  89-)  B    0.17 LOW
 951 PRO   (  19-)  C    0.16 LOW
 972 PRO   (  40-)  C    0.14 LOW
1140 PRO   (  89-)  E    0.20 LOW
1545 PRO   (  19-)  F    0.15 LOW
1566 PRO   (  40-)  F    0.16 LOW
1698 PRO   (  49-)  H    0.18 LOW
2143 PRO   (  19-)  I    0.15 LOW
2164 PRO   (  40-)  I    0.12 LOW
2272 PRO   (  19-)  J    0.13 LOW
2293 PRO   (  40-)  J    0.12 LOW
2425 PRO   (  49-)  K    0.19 LOW
2465 PRO   (  89-)  K    0.18 LOW
2870 PRO   (  19-)  M    0.17 LOW
2891 PRO   (  40-)  M    0.12 LOW
3468 PRO   (  19-)  P    0.17 LOW
3489 PRO   (  40-)  P    0.12 LOW
3657 PRO   (  89-)  R    0.15 LOW
3744 PRO   ( 176-)  R    0.19 LOW
4083 PRO   (  40-)  T    0.13 LOW
4213 PRO   (  50-)  V    0.17 LOW
4252 PRO   (  89-)  V    0.18 LOW
4657 PRO   (  19-)  W    0.16 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].

  36 PRO   (  46-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
  40 PRO   (  50-)  A  -127.2 half-chair C-delta/C-gamma (-126 degrees)
  79 PRO   (  89-)  A    35.3 envelop C-delta (36 degrees)
 253 PRO   ( 263-)  A   -64.1 envelop C-beta (-72 degrees)
 503 PRO   (  46-)  B  -123.2 half-chair C-delta/C-gamma (-126 degrees)
 667 PRO   ( 210-)  B   100.6 envelop C-beta (108 degrees)
 867 PRO   ( 410-)  B  -113.2 envelop C-gamma (-108 degrees)
1012 PRO   (  80-)  C  -124.4 half-chair C-delta/C-gamma (-126 degrees)
1055 PRO   ( 128-)  C   115.6 envelop C-beta (108 degrees)
1097 PRO   (  46-)  E  -119.2 half-chair C-delta/C-gamma (-126 degrees)
1101 PRO   (  50-)  E  -130.7 half-chair C-delta/C-gamma (-126 degrees)
1227 PRO   ( 176-)  E  -114.0 envelop C-gamma (-108 degrees)
1314 PRO   ( 263-)  E   -58.1 half-chair C-beta/C-alpha (-54 degrees)
1606 PRO   (  80-)  F  -126.6 half-chair C-delta/C-gamma (-126 degrees)
1649 PRO   ( 128-)  F   110.7 envelop C-beta (108 degrees)
1695 PRO   (  46-)  H  -113.4 envelop C-gamma (-108 degrees)
1699 PRO   (  50-)  H  -119.2 half-chair C-delta/C-gamma (-126 degrees)
1738 PRO   (  89-)  H    30.9 envelop C-delta (36 degrees)
1825 PRO   ( 176-)  H  -114.1 envelop C-gamma (-108 degrees)
1912 PRO   ( 263-)  H   -50.6 half-chair C-beta/C-alpha (-54 degrees)
2204 PRO   (  80-)  I  -121.3 half-chair C-delta/C-gamma (-126 degrees)
2247 PRO   ( 128-)  I   113.5 envelop C-beta (108 degrees)
2333 PRO   (  80-)  J  -121.6 half-chair C-delta/C-gamma (-126 degrees)
2376 PRO   ( 128-)  J   113.7 envelop C-beta (108 degrees)
2422 PRO   (  46-)  K  -120.7 half-chair C-delta/C-gamma (-126 degrees)
2426 PRO   (  50-)  K  -128.6 half-chair C-delta/C-gamma (-126 degrees)
2639 PRO   ( 263-)  K   -56.6 half-chair C-beta/C-alpha (-54 degrees)
2931 PRO   (  80-)  M  -129.5 half-chair C-delta/C-gamma (-126 degrees)
2974 PRO   ( 128-)  M   116.3 envelop C-beta (108 degrees)
3020 PRO   (  46-)  O  -116.2 envelop C-gamma (-108 degrees)
3024 PRO   (  50-)  O  -129.1 half-chair C-delta/C-gamma (-126 degrees)
3063 PRO   (  89-)  O    37.2 envelop C-delta (36 degrees)
3237 PRO   ( 263-)  O   -54.1 half-chair C-beta/C-alpha (-54 degrees)
3529 PRO   (  80-)  P  -122.3 half-chair C-delta/C-gamma (-126 degrees)
3572 PRO   ( 128-)  P   114.7 envelop C-beta (108 degrees)
3614 PRO   (  46-)  R  -120.7 half-chair C-delta/C-gamma (-126 degrees)
3618 PRO   (  50-)  R  -124.4 half-chair C-delta/C-gamma (-126 degrees)
3831 PRO   ( 263-)  R   -61.1 half-chair C-beta/C-alpha (-54 degrees)
4062 PRO   (  19-)  T  -114.2 envelop C-gamma (-108 degrees)
4123 PRO   (  80-)  T  -125.7 half-chair C-delta/C-gamma (-126 degrees)
4166 PRO   ( 128-)  T   109.9 envelop C-beta (108 degrees)
4209 PRO   (  46-)  V  -115.9 envelop C-gamma (-108 degrees)
4339 PRO   ( 176-)  V  -117.0 envelop C-gamma (-108 degrees)
4426 PRO   ( 263-)  V   -52.8 half-chair C-beta/C-alpha (-54 degrees)
4678 PRO   (  40-)  W   -61.7 half-chair C-beta/C-alpha (-54 degrees)
4718 PRO   (  80-)  W  -126.1 half-chair C-delta/C-gamma (-126 degrees)
4761 PRO   ( 128-)  W   111.0 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 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 906 CYS   ( 449-)  B      SG   <->   916 CYS   ( 459-)  B      SG   0.68    2.77  INTRA
2825 CYS   ( 449-)  K      SG   <->  2835 CYS   ( 459-)  K      SG   0.64    2.81  INTRA
3423 CYS   ( 449-)  O      SG   <->  3433 CYS   ( 459-)  O      SG   0.62    2.83  INTRA
4017 CYS   ( 449-)  R      SG   <->  4027 CYS   ( 459-)  R      SG   0.61    2.84  INTRA
4612 CYS   ( 449-)  V      SG   <->  4622 CYS   ( 459-)  V      SG   0.60    2.85  INTRA
 439 CYS   ( 449-)  A      SG   <->   449 CYS   ( 459-)  A      SG   0.60    2.85  INTRA
1500 CYS   ( 449-)  E      SG   <->  1510 CYS   ( 459-)  E      SG   0.59    2.86  INTRA
2098 CYS   ( 449-)  H      SG   <->  2108 CYS   ( 459-)  H      SG   0.58    2.87  INTRA
2126 MET   (   2-)  I      SD   <->  4860 HOH   (2068 )  I      O    0.54    2.46  INTRA BF
1072 ARG   (  21-)  E      NH2  <->  1102 GLU   (  51-)  E    A OE1  0.51    2.19  INTRA
2643 HIS   ( 267-)  K      CD2  <->  2653 ASN   ( 277-)  K      ND2  0.50    2.60  INTRA BL
3579 ALA   (  11-)  R      N    <->  4866 HOH   (2001 )  R      O    0.46    2.24  INTRA
1348 MET   ( 297-)  E      SD   <->  4857 HOH   (2110 )  E      O    0.46    2.54  INTRA
 257 HIS   ( 267-)  A      CD2  <->   267 ASN   ( 277-)  A      ND2  0.46    2.64  INTRA BL
1318 HIS   ( 267-)  E      CD2  <->  1328 ASN   ( 277-)  E      ND2  0.46    2.64  INTRA BL
2836 GLU   ( 460-)  K      CB   <->  4862 HOH   (2174 )  K      O    0.46    2.34  INTRA
3157 LYS   ( 183-)  O      NZ   <->  4864 HOH   (2077 )  O      O    0.45    2.25  INTRA
3737 LEU   ( 169-)  R      CB   <->  4866 HOH   (2077 )  R      O    0.44    2.36  INTRA
2202 ARG   (  78-)  I      CD   <->  4860 HOH   (2039 )  I      O    0.44    2.36  INTRA
4028 GLU   ( 460-)  R      CG   <->  4866 HOH   (2168 )  R      O    0.43    2.37  INTRA
3241 HIS   ( 267-)  O      CD2  <->  3251 ASN   ( 277-)  O      ND2  0.43    2.67  INTRA BL
4502 ARG   ( 339-)  V      NH1  <->  4868 HOH   (2139 )  V      O    0.43    2.27  INTRA
3835 HIS   ( 267-)  R      CD2  <->  3845 ASN   ( 277-)  R      ND2  0.42    2.68  INTRA BL
3610 MET   (  42-)  R      SD   <->  4866 HOH   (2020 )  R      O    0.42    2.58  INTRA
 724 HIS   ( 267-)  B      CD2  <->   734 ASN   ( 277-)  B      ND2  0.42    2.68  INTRA BL
And so on for a total of 548 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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: M

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: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

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.

2929 ARG   (  78-)  M      -6.77
4716 ARG   (  78-)  W      -6.69
1604 ARG   (  78-)  F      -6.66
2202 ARG   (  78-)  I      -6.57
4121 ARG   (  78-)  T      -6.46
2982 LYS   (   8-)  O      -6.37
1657 LYS   (   8-)  H      -6.36
2331 ARG   (  78-)  J      -6.14
3527 ARG   (  78-)  P      -6.13
2384 LYS   (   8-)  K      -5.86
4007 ARG   ( 439-)  R      -5.81
4602 ARG   ( 439-)  V      -5.81
 896 ARG   ( 439-)  B      -5.81
3413 ARG   ( 439-)  O      -5.81
2088 ARG   ( 439-)  H      -5.81
2815 ARG   ( 439-)  K      -5.80
1490 ARG   ( 439-)  E      -5.80
 429 ARG   ( 439-)  A      -5.80
1010 ARG   (  78-)  C      -5.79
4614 TRP   ( 451-)  V      -5.73
 441 TRP   ( 451-)  A      -5.71
2827 TRP   ( 451-)  K      -5.71
 908 TRP   ( 451-)  B      -5.69
3425 TRP   ( 451-)  O      -5.68
1502 TRP   ( 451-)  E      -5.68
And so on for a total of 115 lines.

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: 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: 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: 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: 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: 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: 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: 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

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.

1350 ALA   ( 299-)  E   -2.79
 756 ALA   ( 299-)  B   -2.79
3867 ALA   ( 299-)  R   -2.79
4462 ALA   ( 299-)  V   -2.78
1042 VAL   ( 110-)  C   -2.78
 289 ALA   ( 299-)  A   -2.76
3411 LEU   ( 437-)  O   -2.75
1488 LEU   ( 437-)  E   -2.75
4005 LEU   ( 437-)  R   -2.75
4600 LEU   ( 437-)  V   -2.74
 894 LEU   ( 437-)  B   -2.74
1948 ALA   ( 299-)  H   -2.73
2675 ALA   ( 299-)  K   -2.73
4748 VAL   ( 110-)  W   -2.73
3273 ALA   ( 299-)  O   -2.72
2813 LEU   ( 437-)  K   -2.72
2086 LEU   ( 437-)  H   -2.70
1636 VAL   ( 110-)  F   -2.70
 427 LEU   ( 437-)  A   -2.69
4153 VAL   ( 110-)  T   -2.66
  97 LEU   ( 107-)  A   -2.63
1756 LEU   ( 107-)  H   -2.61
2483 LEU   ( 107-)  K   -2.59
3081 LEU   ( 107-)  O   -2.58
1158 LEU   ( 107-)  E   -2.57
 564 LEU   ( 107-)  B   -2.57
4270 LEU   ( 107-)  V   -2.57
3675 LEU   ( 107-)  R   -2.56
2360 GLN   ( 107-)  J   -2.53

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

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: M

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: R

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

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.

4855 HOH   (2016 )  B      O
4855 HOH   (2017 )  B      O
4856 HOH   (2008 )  C      O
4856 HOH   (2019 )  C      O
4856 HOH   (2034 )  C      O
4856 HOH   (2051 )  C      O
4856 HOH   (2052 )  C      O
4856 HOH   (2053 )  C      O
4857 HOH   (2023 )  E      O
4857 HOH   (2167 )  E      O
4858 HOH   (2004 )  F      O
4858 HOH   (2022 )  F      O
4858 HOH   (2023 )  F      O
4858 HOH   (2041 )  F      O
4858 HOH   (2044 )  F      O
4859 HOH   (2123 )  H      O
4859 HOH   (2141 )  H      O
4860 HOH   (2026 )  I      O
4860 HOH   (2027 )  I      O
4860 HOH   (2053 )  I      O
4861 HOH   (2009 )  J      O
4862 HOH   (2041 )  K      O
4863 HOH   (2047 )  M      O
4864 HOH   (2036 )  O      O
4864 HOH   (2167 )  O      O
4865 HOH   (2016 )  P      O
4865 HOH   (2019 )  P      O
4866 HOH   (2163 )  R      O
4868 HOH   (2003 )  V      O
4868 HOH   (2042 )  V      O
4869 HOH   (2018 )  W      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.

 143 HIS   ( 153-)  A
 146 GLN   ( 156-)  A
 219 GLN   ( 229-)  A
 228 HIS   ( 238-)  A
 231 ASN   ( 241-)  A
 257 HIS   ( 267-)  A
 267 ASN   ( 277-)  A
 294 GLN   ( 304-)  A
 317 HIS   ( 327-)  A
 376 HIS   ( 386-)  A
 410 ASN   ( 420-)  A
 422 ASN   ( 432-)  A
 610 HIS   ( 153-)  B
 613 GLN   ( 156-)  B
 686 GLN   ( 229-)  B
 695 HIS   ( 238-)  B
 698 ASN   ( 241-)  B
 724 HIS   ( 267-)  B
 734 ASN   ( 277-)  B
 761 GLN   ( 304-)  B
 784 HIS   ( 327-)  B
 843 HIS   ( 386-)  B
 877 ASN   ( 420-)  B
 889 ASN   ( 432-)  B
 941 ASN   (   9-)  C
And so on for a total of 131 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.

  55 THR   (  65-)  A      OG1
  57 THR   (  67-)  A      N
  86 GLN   (  96-)  A      N
 157 ARG   ( 167-)  A      N
 165 LYS   ( 175-)  A      N
 165 LYS   ( 175-)  A      NZ
 168 LEU   ( 178-)  A      N
 201 PHE   ( 211-)  A      N
 207 ARG   ( 217-)  A      NH1
 229 TYR   ( 239-)  A      OH
 236 THR   ( 246-)  A      N
 275 ARG   ( 285-)  A      NH1
 285 ARG   ( 295-)  A      NE
 285 ARG   ( 295-)  A      NH1
 293 ARG   ( 303-)  A      NE
 297 HIS   ( 307-)  A      N
 324 LYS   ( 334-)  A      NZ
 356 GLN   ( 366-)  A      NE2
 363 GLY   ( 373-)  A      N
 369 SER   ( 379-)  A      N
 391 GLN   ( 401-)  A      NE2
 394 GLY   ( 404-)  A      N
 403 ASN   ( 413-)  A      ND2
 444 GLU   ( 454-)  A      N
 522 THR   (  65-)  B      OG1
And so on for a total of 295 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.

 148 GLU   ( 158-)  A      OE1
 258 ASP   ( 268-)  A      OD1
 258 ASP   ( 268-)  A      OD2
 282 HIS   ( 292-)  A      NE2
 725 ASP   ( 268-)  B      OD1
 725 ASP   ( 268-)  B      OD2
 749 HIS   ( 292-)  B      NE2
1319 ASP   ( 268-)  E      OD1
1319 ASP   ( 268-)  E      OD2
1343 HIS   ( 292-)  E      NE2
1452 GLN   ( 401-)  E      OE1
1917 ASP   ( 268-)  H      OD1
1941 HIS   ( 292-)  H      NE2
2644 ASP   ( 268-)  K      OD1
2644 ASP   ( 268-)  K      OD2
2678 ASP   ( 302-)  K      OD1
3242 ASP   ( 268-)  O      OD1
3242 ASP   ( 268-)  O      OD2
3726 GLU   ( 158-)  R      OE1
3836 ASP   ( 268-)  R      OD1
3836 ASP   ( 268-)  R      OD2
3860 HIS   ( 292-)  R      NE2
3969 GLN   ( 401-)  R      OE1
4431 ASP   ( 268-)  V      OD1
4431 ASP   ( 268-)  V      OD2
4564 GLN   ( 401-)  V      OE1

Warning: Unusual water packing

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

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

4854 HOH   (2023 )  A      O  0.88  K  4 ION-B NCS 4/4
4854 HOH   (2098 )  A      O  0.94  K  4 NCS 6/6
4855 HOH   (2074 )  B      O  0.90  K  4 NCS 6/6
4855 HOH   (2080 )  B      O  1.03  K  4 NCS 7/7
4857 HOH   (2082 )  E      O  0.92  K  4 NCS 7/7
4859 HOH   (2074 )  H      O  1.07  K  4 NCS 7/7
4859 HOH   (2126 )  H      O  0.89  K  4 NCS 3/3
4864 HOH   (2151 )  O      O  1.10  K  5 ION-B NCS 1/1
4866 HOH   (2027 )  R      O  0.85  K  5 NCS 5/5
4867 HOH   (2022 )  T      O  0.91  K  4 H2O-B NCS 5/5

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.

  62 ASP   (  72-)  A   H-bonding suggests Asn; Ligand-contact
 258 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 292 ASP   ( 302-)  A   H-bonding suggests Asn; Ligand-contact
 529 ASP   (  72-)  B   H-bonding suggests Asn; Ligand-contact
 725 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 759 ASP   ( 302-)  B   H-bonding suggests Asn
 979 ASP   (  47-)  C   H-bonding suggests Asn; but Alt-Rotamer
1123 ASP   (  72-)  E   H-bonding suggests Asn; Ligand-contact
1319 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1353 ASP   ( 302-)  E   H-bonding suggests Asn
1557 ASP   (  31-)  F   H-bonding suggests Asn
1721 ASP   (  72-)  H   H-bonding suggests Asn; Ligand-contact
1872 GLU   ( 223-)  H   H-bonding suggests Gln
1917 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
1951 ASP   ( 302-)  H   H-bonding suggests Asn
2155 ASP   (  31-)  I   H-bonding suggests Asn
2171 ASP   (  47-)  I   H-bonding suggests Asn; but Alt-Rotamer
2284 ASP   (  31-)  J   H-bonding suggests Asn
2448 ASP   (  72-)  K   H-bonding suggests Asn; Ligand-contact
2599 GLU   ( 223-)  K   H-bonding suggests Gln
2644 ASP   ( 268-)  K   H-bonding suggests Asn; but Alt-Rotamer
2678 ASP   ( 302-)  K   H-bonding suggests Asn
2882 ASP   (  31-)  M   H-bonding suggests Asn
2914 ASP   (  63-)  M   H-bonding suggests Asn; Ligand-contact
3046 ASP   (  72-)  O   H-bonding suggests Asn; Ligand-contact
3197 GLU   ( 223-)  O   H-bonding suggests Gln
3242 ASP   ( 268-)  O   H-bonding suggests Asn; but Alt-Rotamer
3480 ASP   (  31-)  P   H-bonding suggests Asn
3496 ASP   (  47-)  P   H-bonding suggests Asn; but Alt-Rotamer
3512 ASP   (  63-)  P   H-bonding suggests Asn; Ligand-contact
3640 ASP   (  72-)  R   H-bonding suggests Asn; Ligand-contact
3791 GLU   ( 223-)  R   H-bonding suggests Gln
3836 ASP   ( 268-)  R   H-bonding suggests Asn; but Alt-Rotamer
3870 ASP   ( 302-)  R   H-bonding suggests Asn
4074 ASP   (  31-)  T   H-bonding suggests Asn
4235 ASP   (  72-)  V   H-bonding suggests Asn; Ligand-contact
4431 ASP   ( 268-)  V   H-bonding suggests Asn; but Alt-Rotamer
4669 ASP   (  31-)  W   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.901
  2nd generation packing quality :  -0.145
  Ramachandran plot appearance   :  -0.639
  chi-1/chi-2 rotamer normality  :  -2.009
  Backbone conformation          :  -0.331

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.586 (tight)
  Bond angles                    :   0.750
  Omega angle restraints         :   1.106
  Side chain planarity           :   0.543 (tight)
  Improper dihedral distribution :   0.776
  B-factor distribution          :   0.432
  Inside/Outside distribution    :   1.054

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.586 (tight)
  Bond angles                    :   0.750
  Omega angle restraints         :   1.106
  Side chain planarity           :   0.543 (tight)
  Improper dihedral distribution :   0.776
  B-factor distribution          :   0.432
  Inside/Outside distribution    :   1.054
==============

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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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Ramachandran plot
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Symmetry Checks
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Ion Checks
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    M.Nayal and E.Di Cera,
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    P.Mueller, S.Koepke and G.M.Sheldrick,
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Checking checks
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      Who checks the checkers
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