WHAT IF Check report

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

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

Verification log for pdb3po2.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

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

The CRYST1 cell dimensions

    A    = 224.570  B   = 394.550  C    = 282.140
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 224.570  B   = 226.992  C    = 282.140
    Alpha=  90.000  Beta=  90.000  Gamma=  60.352

Dimensions of the conventional cell

    A    = 226.992  B   = 226.992  C    = 282.140
    Alpha=  90.000  Beta=  90.000  Gamma= 120.705

Transformation to conventional cell

 | -0.500000 -0.500000  0.000000|
 | -0.500000  0.500000  0.000000|
 |  0.000000  0.000000 -1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: HEXAGONAL

Space group name: C 2 2 21

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

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

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 2 2 21
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very high

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

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

Molecular weight of all polymer chains: 460911.219
Volume of the Unit Cell V= 24996296.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 13.558
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 5.880 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

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.

4001 ACT   (1734-)  A  -
4002 EPE   ( 222-)  A  -
4003 PEG   ( 172-)  G  -

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

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

Warning: Missing atoms

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

1699 LYS   ( 345-)  B      CG
1699 LYS   ( 345-)  B      CD
1699 LYS   ( 345-)  B      CE
1699 LYS   ( 345-)  B      NZ
2819 ARG   (  11-)  D      CG
2819 ARG   (  11-)  D      CD
2819 ARG   (  11-)  D      NE
2819 ARG   (  11-)  D      CZ
2819 ARG   (  11-)  D      NH1
2819 ARG   (  11-)  D      NH2
2825 LYS   (  17-)  D      CG
2825 LYS   (  17-)  D      CD
2825 LYS   (  17-)  D      CE
2825 LYS   (  17-)  D      NZ

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.

   2 GLN   (   4-)  A    High
   3 GLN   (   5-)  A    High
   4 TYR   (   6-)  A    High
   6 SER   (   8-)  A    High
  10 ARG   (  12-)  A    High
  13 LYS   (  15-)  A    High
  14 GLU   (  16-)  A    High
  21 SER   (  23-)  A    High
  22 PRO   (  24-)  A    High
  23 GLU   (  25-)  A    High
  24 GLU   (  26-)  A    High
  26 ARG   (  28-)  A    High
  28 ILE   (  30-)  A    High
  29 SER   (  31-)  A    High
  32 LYS   (  34-)  A    High
  34 ARG   (  36-)  A    High
  35 PHE   (  37-)  A    High
  36 PRO   (  38-)  A    High
  37 GLU   (  39-)  A    High
  38 THR   (  40-)  A    High
  39 MET   (  41-)  A    High
  40 ASP   (  42-)  A    High
  41 GLU   (  43-)  A    High
  42 THR   (  44-)  A    High
  43 GLN   (  45-)  A    High
And so on for a total of 3249 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

3892 ALA   ( 115-)  K

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: 28

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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

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.

  26 ARG   (  28-)  A
  61 ARG   (  63-)  A
1690 ARG   ( 336-)  B
1691 ARG   ( 337-)  B
1822 ARG   ( 476-)  B
2821 ARG   (  13-)  D

Warning: Tyrosine convention problem

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

 373 TYR   ( 383-)  A
 394 TYR   ( 404-)  A
 407 TYR   ( 417-)  A
 418 TYR   ( 428-)  A
 455 TYR   ( 465-)  A
 468 TYR   ( 478-)  A
 794 TYR   ( 804-)  A
 842 TYR   ( 852-)  A
 887 TYR   ( 897-)  A
1025 TYR   (1035-)  A
1105 TYR   (1119-)  A
1265 TYR   (1298-)  A
1316 TYR   (1349-)  A
1420 TYR   (1453-)  A
1459 TYR   (  57-)  B
1479 TYR   (  96-)  B
1496 TYR   ( 113-)  B
1534 TYR   ( 180-)  B
1544 TYR   ( 190-)  B
1556 TYR   ( 202-)  B
1657 TYR   ( 303-)  B
1832 TYR   ( 486-)  B
2029 TYR   ( 692-)  B
2129 TYR   ( 798-)  B
2142 TYR   ( 811-)  B
And so on for a total of 54 lines.

Warning: Phenylalanine convention problem

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

  17 PHE   (  19-)  A
  20 PHE   (  22-)  A
  35 PHE   (  37-)  A
  89 PHE   (  91-)  A
  93 PHE   (  95-)  A
 201 PHE   ( 211-)  A
 214 PHE   ( 224-)  A
 218 PHE   ( 228-)  A
 254 PHE   ( 264-)  A
 337 PHE   ( 347-)  A
 458 PHE   ( 468-)  A
 472 PHE   ( 482-)  A
 530 PHE   ( 540-)  A
 581 PHE   ( 591-)  A
 636 PHE   ( 646-)  A
 711 PHE   ( 721-)  A
 767 PHE   ( 777-)  A
 769 PHE   ( 779-)  A
 777 PHE   ( 787-)  A
 805 PHE   ( 815-)  A
 883 PHE   ( 893-)  A
 937 PHE   ( 947-)  A
 961 PHE   ( 971-)  A
1074 PHE   (1084-)  A
1076 PHE   (1086-)  A
And so on for a total of 85 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.

  53 ASP   (  55-)  A
  60 ASP   (  62-)  A
 149 ASP   ( 151-)  A
 185 ASP   ( 195-)  A
 250 ASP   ( 260-)  A
 251 ASP   ( 261-)  A
 352 ASP   ( 362-)  A
 413 ASP   ( 423-)  A
 471 ASP   ( 481-)  A
 473 ASP   ( 483-)  A
 475 ASP   ( 485-)  A
 528 ASP   ( 538-)  A
 534 ASP   ( 544-)  A
 545 ASP   ( 555-)  A
 780 ASP   ( 790-)  A
 864 ASP   ( 874-)  A
 899 ASP   ( 909-)  A
1113 ASP   (1127-)  A
1174 ASP   (1198-)  A
1182 ASP   (1206-)  A
1199 ASP   (1223-)  A
1209 ASP   (1233-)  A
1224 ASP   (1257-)  A
1276 ASP   (1309-)  A
1290 ASP   (1323-)  A
And so on for a total of 59 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.

 147 GLU   ( 149-)  A
 186 GLU   ( 196-)  A
 188 GLU   ( 198-)  A
 195 GLU   ( 205-)  A
 196 GLU   ( 206-)  A
 244 GLU   ( 254-)  A
 270 GLU   ( 280-)  A
 280 GLU   ( 290-)  A
 476 GLU   ( 486-)  A
 490 GLU   ( 500-)  A
 583 GLU   ( 593-)  A
 626 GLU   ( 636-)  A
 668 GLU   ( 678-)  A
 761 GLU   ( 771-)  A
 836 GLU   ( 846-)  A
 869 GLU   ( 879-)  A
 904 GLU   ( 914-)  A
 908 GLU   ( 918-)  A
 921 GLU   ( 931-)  A
 995 GLU   (1005-)  A
1064 GLU   (1074-)  A
1089 GLU   (1103-)  A
1125 GLU   (1139-)  A
1210 GLU   (1234-)  A
1222 GLU   (1255-)  A
And so on for a total of 96 lines.

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

3984 BRU   (  22-)  T

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.

   2 GLN   (   4-)  A      N   -C     1.41    4.2
  28 ILE   (  30-)  A      CG1  CD1   1.68    4.3
  53 ASP   (  55-)  A      CA   C     1.41   -5.5
  55 ARG   (  57-)  A      N   -C     1.47    7.1
 389 HIS   ( 399-)  A      N   -C     1.41    4.3
 414 ILE   ( 424-)  A      CG1  CD1   1.34   -4.4
2213 THR   ( 882-)  B      CA   C     1.63    4.9
2213 THR   ( 882-)  B      CA   CB    1.62    4.3
2266 ILE   ( 948-)  B      CG1  CD1   1.69    4.6
2673 ILE   ( 133-)  C      CG1  CD1   1.34   -4.5
2832 ALA   (  24-)  D      CA   C     1.62    4.6
3291 PHE   (   2-)  G      N   -C     1.43    4.8
3334 ILE   (  45-)  G      CG1  CD1   1.67    4.1
3350 ILE   (  61-)  G      CG1  CD1   1.35   -4.2
3440 ILE   ( 151-)  G      CG1  CD1   1.75    6.0
3946 DCYT  (   8-)  N      C1'  N1    1.52    4.4
3950 DCYT  (  12-)  N      C1'  N1    1.52    4.5
3952 OCYT  (   5-)  P      C1'  N1    1.57    8.2
3953 OCYT  (   6-)  P      C1'  N1    1.56    7.4
3954 OCYT  (   7-)  P      C1'  N1    1.55    6.7
3954 OCYT  (   7-)  P      N1   C2    1.44    4.4
3955 OCYT  (   8-)  P      C1'  N1    1.54    6.1
3956 OCYT  (   9-)  P      C1'  N1    1.54    6.2
3957 OCYT  (  10-)  P      C1'  N1    1.52    4.4
3958 OCYT  (  11-)  P      C1'  N1    1.54    6.0
3959 OCYT  (  12-)  P      C1'  N1    1.55    6.6
3960 OCYT  (  13-)  P      C1'  N1    1.53    4.9
3961 OCYT  (  14-)  P      C1'  N1    1.53    4.8
3962 OCYT  (  15-)  P      C1'  N1    1.53    5.3
3963 OCYT  (  16-)  P      C1'  N1    1.53    4.9
3964 OCYT  (  17-)  P      C1'  N1    1.54    5.5
3965 OCYT  (  18-)  P      C1'  N1    1.52    4.0
3966 OCYT  (  19-)  P      C1'  N1    1.53    4.7
3969 DCYT  (   7-)  T      C1'  N1    1.53    5.0
3982 DTHY  (  20-)  T      C1'  N1    1.53    4.1
3983 DGUA  (  21-)  T      N9   C4    1.41    4.1
3983 DGUA  (  21-)  T      N3   C4    1.39    5.0
3983 DGUA  (  21-)  T      C2   N3    1.36    4.4
3985 DTHY  (  23-)  T      C1'  N1    1.56    6.3

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

 |  0.997091  0.000055  0.000165|
 |  0.000055  0.996826 -0.000204|
 |  0.000165 -0.000204  0.997054|
Proposed new scale matrix

 |  0.004466  0.000000  0.000000|
 |  0.000000  0.002543  0.000000|
 |  0.000000  0.000000  0.003554|
With corresponding cell

    A    = 223.914  B   = 393.225  C    = 281.336
    Alpha=  90.004  Beta=  90.003  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 224.568  B   = 394.477  C    = 282.167
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1389.931
(Under-)estimated Z-score: 27.477

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.

   2 GLN   (   4-)  A     -C    N    CA  131.47    5.4
  17 PHE   (  19-)  A      CA   CB   CG  108.87   -4.9
  24 GLU   (  26-)  A      CB   CG   CD  120.32    4.5
  40 ASP   (  42-)  A     -C    N    CA  131.57    5.5
  40 ASP   (  42-)  A      CA   CB   CG  118.44    5.8
  41 GLU   (  43-)  A     -C    N    CA  130.27    4.8
  42 THR   (  44-)  A      C    CA   CB  118.02    4.2
  46 ALA   (  48-)  A     -C    N    CA  130.36    4.8
  52 ASN   (  54-)  A      CA   CB   CG  118.72    6.1
  53 ASP   (  55-)  A     -C    N    CA  136.82    8.4
  53 ASP   (  55-)  A      N    CA   CB  123.37    7.6
  54 PRO   (  56-)  A     -CA  -C    N   106.98   -6.6
  55 ARG   (  57-)  A     -C    N    CA  138.79    9.5
  60 ASP   (  62-)  A      CA   CB   CG  119.11    6.5
  62 ASN   (  64-)  A     -C    N    CA  133.25    6.4
  63 LEU   (  65-)  A     -C    N    CA  129.57    4.4
  72 MET   (  74-)  A     -C    N    CA  131.94    5.7
  89 PHE   (  91-)  A      CA   CB   CG  118.42    4.6
 128 ASP   ( 130-)  A      CA   CB   CG  116.83    4.2
 167 ASN   ( 169-)  A     -C    N    CA  130.46    4.9
 171 THR   ( 173-)  A      C    CA   CB  120.07    5.2
 186 GLU   ( 196-)  A     -C    N    CA  129.27    4.2
 196 GLU   ( 206-)  A     -C    N    CA  129.21    4.2
 208 ASP   ( 218-)  A      CA   CB   CG  119.19    6.6
 209 PHE   ( 219-)  A      CA   CB   CG  120.80    7.0
And so on for a total of 413 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  26 ARG   (  28-)  A
  53 ASP   (  55-)  A
  60 ASP   (  62-)  A
  61 ARG   (  63-)  A
 147 GLU   ( 149-)  A
 149 ASP   ( 151-)  A
 185 ASP   ( 195-)  A
 186 GLU   ( 196-)  A
 188 GLU   ( 198-)  A
 195 GLU   ( 205-)  A
 196 GLU   ( 206-)  A
 244 GLU   ( 254-)  A
 250 ASP   ( 260-)  A
 251 ASP   ( 261-)  A
 270 GLU   ( 280-)  A
 280 GLU   ( 290-)  A
 352 ASP   ( 362-)  A
 413 ASP   ( 423-)  A
 471 ASP   ( 481-)  A
 473 ASP   ( 483-)  A
 475 ASP   ( 485-)  A
 476 GLU   ( 486-)  A
 490 GLU   ( 500-)  A
 528 ASP   ( 538-)  A
 534 ASP   ( 544-)  A
And so on for a total of 161 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.

  33 ILE   (  35-)  A      CA    -6.5    23.43    33.24
  52 ASN   (  54-)  A      CA    -6.1    22.00    33.59
  53 ASP   (  55-)  A      CA    -7.6    18.63    33.73
  53 ASP   (  55-)  A      C      8.7    13.32    -0.01
  94 ILE   (  96-)  A      CA    -6.0    24.15    33.24
 312 VAL   ( 322-)  A      CA    -6.6    23.68    33.23
 389 HIS   ( 399-)  A      CA    -7.2    20.90    34.11
 390 PRO   ( 400-)  A      C     -6.4    -9.71     0.42
 441 HIS   ( 451-)  A      CA     6.5    46.11    34.11
 580 ARG   ( 590-)  A      CA    -6.2    23.79    33.91
1104 VAL   (1118-)  A      CA    -6.1    24.35    33.23
2062 VAL   ( 731-)  B      CA    -6.6    23.72    33.23
2294 ILE   ( 976-)  B      CA    -7.7    21.67    33.24
2498 PHE   (1180-)  B      CA    -7.2    22.40    33.98
3353 THR   (  64-)  G      CA    -7.9    20.71    33.84
3518 ILE   (  59-)  H      CA    -7.6    21.69    33.24
3595 THR   (   3-)  I      CA    -6.7    22.71    33.84
3644 ILE   (  52-)  I      CA    -6.9    22.75    33.24
3840 VAL   (  63-)  K      CA    -6.1    24.41    33.23
3931 LEU   (  64-)  L      CA    -8.0    22.01    34.19
The average deviation= 1.431

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.

2579 ALA   (  39-)  C   10.32
1370 GLU   (1403-)  A    9.68
1371 GLU   (1404-)  A    5.78
3717 VAL   (   5-)  J    5.39
1372 THR   (1405-)  A    5.15
2723 TRP   ( 183-)  C    5.12
 311 PRO   ( 321-)  A    5.09
1843 ARG   ( 497-)  B    4.96
2448 PHE   (1130-)  B    4.81
3323 VAL   (  34-)  G    4.79
 462 LEU   ( 472-)  A    4.74
2492 LYS   (1174-)  B    4.66
2499 GLU   (1181-)  B    4.63
 887 TYR   ( 897-)  A    4.62
3023 GLU   (  36-)  E    4.59
1650 GLU   ( 296-)  B    4.52
3291 PHE   (   2-)  G    4.51
 322 LYS   ( 332-)  A    4.46
3718 ARG   (   6-)  J    4.36
 714 GLU   ( 724-)  A    4.30
 485 GLU   ( 495-)  A    4.30
2252 LYS   ( 934-)  B    4.27
2232 PRO   ( 901-)  B    4.25
3164 ARG   ( 177-)  E    4.23
3729 LYS   (  17-)  J    4.20
2834 THR   (  26-)  D    4.19
3537 ALA   (  90-)  H    4.13
 865 ALA   ( 875-)  A    4.13
2160 CYS   ( 829-)  B    4.10
3730 TRP   (  18-)  J    4.09
1898 MET   ( 552-)  B    4.07
2474 ASP   (1156-)  B    4.07
2837 LEU   (  29-)  D    4.06
1308 ILE   (1341-)  A    4.05
2500 CYS   (1182-)  B    4.04

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.

3767 ASP   (  55-)  J    4.80
1370 GLU   (1403-)  A    4.70
2315 GLU   ( 997-)  B    4.60
 336 ASP   ( 346-)  A    4.16
 435 ASN   ( 445-)  A    4.14

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

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

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

1372 THR   (1405-)  A    -3.6
1073 THR   (1083-)  A    -3.3
3529 PRO   (  82-)  H    -3.0
1693 THR   ( 339-)  B    -2.9
3428 ILE   ( 139-)  G    -2.9
2532 PRO   (1214-)  B    -2.9
  42 THR   (  44-)  A    -2.9
3291 PHE   (   2-)  G    -2.9
1071 LEU   (1081-)  A    -2.9
  54 PRO   (  56-)  A    -2.8
2310 ILE   ( 992-)  B    -2.8
3112 PRO   ( 125-)  E    -2.8
3443 VAL   ( 154-)  G    -2.7
3910 THR   (  43-)  L    -2.7
1718 ILE   ( 364-)  B    -2.7
2695 LEU   ( 155-)  C    -2.7
 325 ARG   ( 335-)  A    -2.7
  63 LEU   (  65-)  A    -2.7
3491 THR   (  32-)  H    -2.7
3921 ARG   (  54-)  L    -2.6
2617 ILE   (  77-)  C    -2.6
1529 ARG   ( 175-)  B    -2.6
 171 THR   ( 173-)  A    -2.6
2213 THR   ( 882-)  B    -2.6
2780 VAL   ( 240-)  C    -2.6
And so on for a total of 227 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.

   2 GLN   (   4-)  A  Poor phi/psi
   3 GLN   (   5-)  A  Poor phi/psi
  39 MET   (  41-)  A  Poor phi/psi
  40 ASP   (  42-)  A  Poor phi/psi
  41 GLU   (  43-)  A  Poor phi/psi
  42 THR   (  44-)  A  Poor phi/psi
  43 GLN   (  45-)  A  Poor phi/psi
  46 ALA   (  48-)  A  Poor phi/psi
  52 ASN   (  54-)  A  Poor phi/psi
  53 ASP   (  55-)  A  Poor phi/psi, PRO omega poor
  55 ARG   (  57-)  A  Poor phi/psi
  63 LEU   (  65-)  A  Poor phi/psi
  66 GLN   (  68-)  A  Poor phi/psi
  72 MET   (  74-)  A  Poor phi/psi
  74 GLU   (  76-)  A  Poor phi/psi
 154 ASP   ( 156-)  A  Poor phi/psi
 167 ASN   ( 169-)  A  Poor phi/psi
 186 GLU   ( 196-)  A  Poor phi/psi
 240 ILE   ( 250-)  A  Poor phi/psi
 243 ASN   ( 253-)  A  Poor phi/psi
 246 GLN   ( 256-)  A  Poor phi/psi
 247 ARG   ( 257-)  A  Poor phi/psi
 248 GLY   ( 258-)  A  Poor phi/psi
 273 GLY   ( 283-)  A  Poor phi/psi
 275 PRO   ( 285-)  A  Poor phi/psi
And so on for a total of 239 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.702

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.

1061 SER   (1071-)  A    0.33
 265 SER   ( 275-)  A    0.36
1037 SER   (1047-)  A    0.36
1283 VAL   (1316-)  A    0.38
1437 SER   (  35-)  B    0.38
2861 SER   (  53-)  D    0.38
1797 LYS   ( 451-)  B    0.38
1281 SER   (1314-)  A    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 GLN   (   5-)  A      0
  17 PHE   (  19-)  A      0
  28 ILE   (  30-)  A      0
  33 ILE   (  35-)  A      0
  34 ARG   (  36-)  A      0
  36 PRO   (  38-)  A      0
  37 GLU   (  39-)  A      0
  38 THR   (  40-)  A      0
  39 MET   (  41-)  A      0
  40 ASP   (  42-)  A      0
  41 GLU   (  43-)  A      0
  42 THR   (  44-)  A      0
  43 GLN   (  45-)  A      0
  45 ARG   (  47-)  A      0
  46 ALA   (  48-)  A      0
  47 LYS   (  49-)  A      0
  48 ILE   (  50-)  A      0
  51 LEU   (  53-)  A      0
  52 ASN   (  54-)  A      0
  53 ASP   (  55-)  A      0
  54 PRO   (  56-)  A      0
  55 ARG   (  57-)  A      0
  56 LEU   (  58-)  A      0
  58 SER   (  60-)  A      0
  60 ASP   (  62-)  A      0
And so on for a total of 1652 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 2.823

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!

 324 GLY   ( 334-)  A   2.52   13
3574 GLY   ( 127-)  H   2.40   13
 248 GLY   ( 258-)  A   1.95   40
1497 PRO   ( 114-)  B   1.88   15
1109 GLY   (1123-)  A   1.84   80
 605 GLY   ( 615-)  A   1.69   14
1327 GLY   (1360-)  A   1.69   80
1108 PRO   (1122-)  A   1.66   10
3170 PRO   ( 183-)  E   1.60   10
 300 GLY   ( 310-)  A   1.54   15
  80 GLY   (  82-)  A   1.51   32

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...

  52 ASN   (  54-)  A   1.99
2824 LYS   (  16-)  D   1.78

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]

 230 PRO   ( 240-)  A    0.16 LOW
2088 PRO   ( 757-)  B    0.18 LOW
3781 PRO   (   4-)  K    0.17 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].

  54 PRO   (  56-)  A    26.5 half-chair N/C-delta (18 degrees)
 187 PRO   ( 197-)  A   -60.6 half-chair C-beta/C-alpha (-54 degrees)
 275 PRO   ( 285-)  A    33.3 envelop C-delta (36 degrees)
 302 PRO   ( 312-)  A   -53.3 half-chair C-beta/C-alpha (-54 degrees)
 311 PRO   ( 321-)  A    99.9 envelop C-beta (108 degrees)
 386 PRO   ( 396-)  A    45.3 half-chair C-delta/C-gamma (54 degrees)
 390 PRO   ( 400-)  A    50.3 half-chair C-delta/C-gamma (54 degrees)
 590 PRO   ( 600-)  A    40.4 envelop C-delta (36 degrees)
 775 PRO   ( 785-)  A    -3.2 envelop N (0 degrees)
 800 PRO   ( 810-)  A   101.1 envelop C-beta (108 degrees)
 945 PRO   ( 955-)  A    51.4 half-chair C-delta/C-gamma (54 degrees)
1166 PRO   (1190-)  A   -28.5 envelop C-alpha (-36 degrees)
1259 PRO   (1292-)  A    45.1 half-chair C-delta/C-gamma (54 degrees)
1585 PRO   ( 231-)  B    46.1 half-chair C-delta/C-gamma (54 degrees)
1587 PRO   ( 233-)  B   -22.0 half-chair C-alpha/N (-18 degrees)
1847 PRO   ( 501-)  B    30.0 envelop C-delta (36 degrees)
1917 PRO   ( 571-)  B    99.3 envelop C-beta (108 degrees)
1921 PRO   ( 575-)  B    37.6 envelop C-delta (36 degrees)
1982 PRO   ( 636-)  B   -43.3 envelop C-alpha (-36 degrees)
2044 PRO   ( 707-)  B    30.5 envelop C-delta (36 degrees)
2049 PRO   ( 712-)  B   -61.1 half-chair C-beta/C-alpha (-54 degrees)
2076 PRO   ( 745-)  B  -121.2 half-chair C-delta/C-gamma (-126 degrees)
2133 PRO   ( 802-)  B    32.0 envelop C-delta (36 degrees)
2258 PRO   ( 940-)  B   -47.8 half-chair C-beta/C-alpha (-54 degrees)
2428 PRO   (1110-)  B  -120.2 half-chair C-delta/C-gamma (-126 degrees)
2532 PRO   (1214-)  B   -23.3 half-chair C-alpha/N (-18 degrees)
2611 PRO   (  71-)  C    47.8 half-chair C-delta/C-gamma (54 degrees)
2722 PRO   ( 182-)  C    52.6 half-chair C-delta/C-gamma (54 degrees)
3112 PRO   ( 125-)  E   -16.1 half-chair C-alpha/N (-18 degrees)
3115 PRO   ( 128-)  E    42.2 envelop C-delta (36 degrees)
3170 PRO   ( 183-)  E   100.4 envelop C-beta (108 degrees)
3309 PRO   (  20-)  G    31.6 envelop C-delta (36 degrees)
3416 PRO   ( 127-)  G   -59.3 half-chair C-beta/C-alpha (-54 degrees)
3476 PRO   (  17-)  H    -5.7 envelop N (0 degrees)
3507 PRO   (  48-)  H    34.6 envelop C-delta (36 degrees)
3529 PRO   (  82-)  H   134.4 half-chair C-beta/C-alpha (126 degrees)
3608 PRO   (  16-)  I    51.8 half-chair C-delta/C-gamma (54 degrees)
3633 PRO   (  41-)  I   -63.9 envelop C-beta (-72 degrees)
3658 PRO   (  66-)  I    51.1 half-chair C-delta/C-gamma (54 degrees)
3661 PRO   (  69-)  I   -63.3 envelop C-beta (-72 degrees)
3668 PRO   (  76-)  I    51.9 half-chair C-delta/C-gamma (54 degrees)
3777 PRO   (  65-)  J    52.8 half-chair C-delta/C-gamma (54 degrees)
3800 PRO   (  23-)  K    33.6 envelop C-delta (36 degrees)
3805 PRO   (  28-)  K    46.4 half-chair C-delta/C-gamma (54 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.

3290 MET   (   1-)  G      SD  <-> 3291 PHE   (   2-)  G      N      0.59    2.61  INTRA BL
  54 PRO   (  56-)  A      O   <->   55 ARG   (  57-)  A      NE     0.50    2.10  INTRA BL
2606 ARG   (  66-)  C      NH2 <-> 3715 VAL   (   3-)  J      O      0.45    2.25  INTRA BL
 459 ARG   ( 469-)  A      NH2 <-> 2309 GLY   ( 991-)  B      O      0.43    2.27  INTRA BL
2331 ASN   (1013-)  B      ND2 <-> 2333 HIS   (1015-)  B      CD2    0.42    2.68  INTRA BL
 861 ASP   ( 871-)  A      OD1 <-> 1333 ARG   (1366-)  A      NH2    0.39    2.31  INTRA BL
2316 ASP   ( 998-)  B      OD1 <-> 2575 ARG   (  35-)  C      NH2    0.38    2.32  INTRA BL
 296 ASN   ( 306-)  A      ND2 <->  311 PRO   ( 321-)  A      O      0.36    2.34  INTRA BL
2178 ASP   ( 847-)  B      OD2 <-> 3783 ARG   (   6-)  K      NH2    0.36    2.34  INTRA BL
   3 GLN   (   5-)  A      O   <-> 2477 ARG   (1159-)  B      NH2    0.34    2.36  INTRA BL
2834 THR   (  26-)  D      N   <-> 2835 LEU   (  27-)  D      N      0.30    2.30  INTRA BL
3037 MET   (  50-)  E      SD  <-> 3038 GLY   (  51-)  E      N      0.30    2.90  INTRA BF
3955 OCYT  (   8-)  P      O2  <-> 3983 DGUA  (  21-)  T      N2     0.29    2.41  INTRA BF
 352 ASP   ( 362-)  A      OD2 <->  449 ARG   ( 459-)  A      NH1    0.27    2.43  INTRA BL
  53 ASP   (  55-)  A      N   <->   54 PRO   (  56-)  A      CD     0.27    2.73  INTRA BL
3599 CYS   (   7-)  I      SG  <-> 3602 CYS   (  10-)  I      CB     0.27    3.13  INTRA BF
 275 PRO   ( 285-)  A      O   <->  277 HIS   ( 287-)  A      N      0.27    2.43  INTRA BF
1175 ARG   (1199-)  A      NH2 <-> 1209 ASP   (1233-)  A      O      0.26    2.44  INTRA BF
 845 THR   ( 855-)  A      CG2 <->  847 ARG   ( 857-)  A      NE     0.25    2.85  INTRA BL
3600 ARG   (   8-)  I      NE  <-> 3601 ASP   (   9-)  I      OD2    0.25    2.45  INTRA BF
3529 PRO   (  82-)  H      O   <-> 3531 ALA   (  84-)  H      N      0.25    2.45  INTRA BF
1876 GLY   ( 530-)  B      O   <-> 1878 ALA   ( 532-)  B      N      0.25    2.45  INTRA BL
2178 ASP   ( 847-)  B      CG  <-> 3783 ARG   (   6-)  K      NH2    0.24    2.86  INTRA BL
1549 CYS   ( 195-)  B      SG  <-> 2114 THR   ( 783-)  B      N      0.23    3.07  INTRA BL
2822 ARG   (  14-)  D      O   <-> 2824 LYS   (  16-)  D      N      0.23    2.47  INTRA BF
And so on for a total of 270 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

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.

1850 ARG   ( 504-)  B      -8.45
2426 ARG   (1108-)  B      -7.48
2061 ARG   ( 730-)  B      -7.25
1937 ARG   ( 591-)  B      -7.21
2540 ARG   (1222-)  B      -7.12
  61 ARG   (  63-)  A      -6.95
2199 MET   ( 868-)  B      -6.92
 993 LYS   (1003-)  A      -6.91
   2 GLN   (   4-)  A      -6.76
3710 ARG   ( 118-)  I      -6.75
2987 LEU   ( 220-)  D      -6.68
3600 ARG   (   8-)  I      -6.68
3909 ARG   (  42-)  L      -6.67
3576 TYR   ( 129-)  H      -6.61
1819 MET   ( 473-)  B      -6.61
2820 ARG   (  12-)  D      -6.58
 991 ARG   (1001-)  A      -6.50
2627 PHE   (  87-)  C      -6.46
3530 GLN   (  83-)  H      -6.40
3527 ARG   (  80-)  H      -6.40
  45 ARG   (  47-)  A      -6.39
1600 LYS   ( 246-)  B      -6.39
 271 HIS   ( 281-)  A      -6.33
1345 GLN   (1378-)  A      -6.32
1145 ARG   (1159-)  A      -6.29
And so on for a total of 111 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.

 387 ASN   ( 397-)  A       389 - HIS    399- ( A)         -4.72
 625 ARG   ( 635-)  A       627 - LYS    637- ( A)         -4.45
1368 SER   (1401-)  A      1371 - GLU   1404- ( A)         -4.38
1441 ARG   (  39-)  B      1443 - LYS     41- ( B)         -4.70
1692 GLY   ( 338-)  B      1695 - LEU    341- ( B)         -4.25
2060 ILE   ( 729-)  B      2062 - VAL    731- ( B)         -5.47
2820 ARG   (  12-)  D      2822 - ARG     14- ( D)         -5.29
2826 VAL   (  18-)  D      2828 - GLU     20- ( D)         -4.62
3154 ARG   ( 167-)  E      3156 - ARG    169- ( E)         -4.24
3709 LYS   ( 117-)  I      3711 - THR    119- ( I)         -5.83

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

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.

 437 GLN   ( 447-)  A   -3.20
2819 ARG   (  11-)  D   -3.04
1853 LYS   ( 507-)  B   -2.85
1407 ALA   (1440-)  A   -2.70
 494 LEU   ( 504-)  A   -2.60
 462 LEU   ( 472-)  A   -2.59
3037 MET   (  50-)  E   -2.58
2470 MET   (1152-)  B   -2.57
2079 ILE   ( 748-)  B   -2.57
2825 LYS   (  17-)  D   -2.52
2447 ARG   (1129-)  B   -2.51

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.

3927 ARG   (  60-)  L     - 3931 LEU   (  64-)  L        -1.80

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

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

  16 GLN   (  18-)  A
  81 HIS   (  83-)  A
 215 ASN   ( 225-)  A
 329 ASN   ( 339-)  A
 389 HIS   ( 399-)  A
 425 HIS   ( 435-)  A
 437 GLN   ( 447-)  A
 441 HIS   ( 451-)  A
 493 GLN   ( 503-)  A
 507 ASN   ( 517-)  A
 538 ASN   ( 548-)  A
 593 ASN   ( 603-)  A
 731 ASN   ( 741-)  A
 747 ASN   ( 757-)  A
 750 GLN   ( 760-)  A
 758 GLN   ( 768-)  A
 776 HIS   ( 786-)  A
 848 ASN   ( 858-)  A
 965 HIS   ( 975-)  A
 984 GLN   ( 994-)  A
1038 ASN   (1048-)  A
1075 HIS   (1085-)  A
1114 GLN   (1128-)  A
1126 HIS   (1140-)  A
1157 GLN   (1171-)  A
And so on for a total of 66 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.

   1 GLY   (   3-)  A      N
   5 SER   (   7-)  A      OG
   6 SER   (   8-)  A      OG
  32 LYS   (  34-)  A      N
  33 ILE   (  35-)  A      N
  35 PHE   (  37-)  A      N
  37 GLU   (  39-)  A      N
  41 GLU   (  43-)  A      N
  47 LYS   (  49-)  A      NZ
  50 GLY   (  52-)  A      N
  52 ASN   (  54-)  A      N
  53 ASP   (  55-)  A      N
  56 LEU   (  58-)  A      N
  59 ILE   (  61-)  A      N
  60 ASP   (  62-)  A      N
  64 LYS   (  66-)  A      N
  65 CYS   (  67-)  A      N
  66 GLN   (  68-)  A      N
  69 GLN   (  71-)  A      N
  70 GLU   (  72-)  A      N
  71 GLY   (  73-)  A      N
  83 ASP   (  85-)  A      N
  86 LYS   (  88-)  A      N
  91 VAL   (  93-)  A      N
 110 LYS   ( 112-)  A      N
And so on for a total of 466 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.

  40 ASP   (  42-)  A      OD1
  52 ASN   (  54-)  A      OD1
 289 HIS   ( 299-)  A      ND1
 435 ASN   ( 445-)  A      OD1
 486 GLU   ( 496-)  A      OE1
 577 HIS   ( 587-)  A      ND1
 621 HIS   ( 631-)  A      NE2
 713 ASN   ( 723-)  A      OD1
 757 GLN   ( 767-)  A      OE1
 776 HIS   ( 786-)  A      ND1
 791 GLU   ( 801-)  A      OE1
 806 HIS   ( 816-)  A      ND1
 916 GLN   ( 926-)  A      OE1
1274 GLU   (1307-)  A      OE1
1334 HIS   (1367-)  A      ND1
1387 ASP   (1420-)  A      OD1
1448 GLN   (  46-)  B      OE1
1449 GLN   (  47-)  B      OE1
1498 GLN   ( 115-)  B      OE1
1548 GLU   ( 194-)  B      OE2
2035 GLU   ( 698-)  B      OE1
2048 GLU   ( 711-)  B      OE2
2173 ASN   ( 842-)  B      OD1
2333 HIS   (1015-)  B      NE2
2343 HIS   (1025-)  B      ND1
2394 HIS   (1076-)  B      ND1
2471 GLU   (1153-)  B      OE1
2691 GLN   ( 151-)  C      OE1
2719 GLU   ( 179-)  C      OE2
2848 HIS   (  40-)  D      ND1
3134 HIS   ( 147-)  E      NE2
3258 GLU   ( 124-)  F      OE1
3442 GLN   ( 153-)  G      OE1
3581 ASN   ( 134-)  H      OD1
3675 ASN   (  83-)  I      OD1
3920 HIS   (  53-)  L      ND1

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+.

3993  MG   (2458-)  A     0.73   1.46 Scores about as good as NA *2
Since there are no waters, the water check has been skipped.

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.

  40 ASP   (  42-)  A   H-bonding suggests Asn; but Alt-Rotamer
  74 GLU   (  76-)  A   H-bonding suggests Gln
 280 GLU   ( 290-)  A   H-bonding suggests Gln; but Alt-Rotamer
 281 GLU   ( 291-)  A   H-bonding suggests Gln
 388 GLU   ( 398-)  A   H-bonding suggests Gln
 486 GLU   ( 496-)  A   H-bonding suggests Gln; but Alt-Rotamer
 682 ASP   ( 692-)  A   H-bonding suggests Asn
 717 ASP   ( 727-)  A   H-bonding suggests Asn; but Alt-Rotamer
 812 GLU   ( 822-)  A   H-bonding suggests Gln
 816 ASP   ( 826-)  A   H-bonding suggests Asn
 920 ASP   ( 930-)  A   H-bonding suggests Asn
 982 ASP   ( 992-)  A   H-bonding suggests Asn
1003 ASP   (1013-)  A   H-bonding suggests Asn
1033 ASP   (1043-)  A   H-bonding suggests Asn; but Alt-Rotamer
1199 ASP   (1223-)  A   H-bonding suggests Asn
1247 GLU   (1280-)  A   H-bonding suggests Gln
1326 ASP   (1359-)  A   H-bonding suggests Asn
1340 ASP   (1373-)  A   H-bonding suggests Asn
1374 GLU   (1407-)  A   H-bonding suggests Gln; but Alt-Rotamer
1463 ASP   (  61-)  B   H-bonding suggests Asn
1708 ASP   ( 354-)  B   H-bonding suggests Asn
1725 GLU   ( 371-)  B   H-bonding suggests Gln
1906 GLU   ( 560-)  B   H-bonding suggests Gln
1989 ASP   ( 643-)  B   H-bonding suggests Asn
2033 GLU   ( 696-)  B   H-bonding suggests Gln; but Alt-Rotamer
2048 GLU   ( 711-)  B   H-bonding suggests Gln; but Alt-Rotamer
2359 GLU   (1041-)  B   H-bonding suggests Gln
2452 GLU   (1134-)  B   H-bonding suggests Gln
2544 GLU   (   4-)  C   H-bonding suggests Gln
2559 ASP   (  19-)  C   H-bonding suggests Asn; but Alt-Rotamer
2618 GLU   (  78-)  C   H-bonding suggests Gln
2721 ASP   ( 181-)  C   H-bonding suggests Asn
2748 GLU   ( 208-)  C   H-bonding suggests Gln
2757 ASP   ( 217-)  C   H-bonding suggests Asn
2808 ASP   ( 268-)  C   H-bonding suggests Asn
2898 GLU   ( 131-)  D   H-bonding suggests Gln
2907 ASP   ( 140-)  D   H-bonding suggests Asn; but Alt-Rotamer
2989 ASP   (   2-)  E   H-bonding suggests Asn
2991 GLU   (   4-)  E   H-bonding suggests Gln
3553 GLU   ( 106-)  H   H-bonding suggests Gln
3601 ASP   (   9-)  I   H-bonding suggests Asn
3666 GLU   (  74-)  I   H-bonding suggests Gln
3728 ASP   (  16-)  J   H-bonding suggests Asn
3815 GLU   (  38-)  K   H-bonding suggests Gln

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 :  -1.010
  2nd generation packing quality :  -1.461
  Ramachandran plot appearance   :  -2.436
  chi-1/chi-2 rotamer normality  :  -4.702 (bad)
  Backbone conformation          :  -0.336

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.691
  Bond angles                    :   1.122
  Omega angle restraints         :   0.513 (tight)
  Side chain planarity           :   1.112
  Improper dihedral distribution :   1.250
  B-factor distribution          :   0.552
  Inside/Outside distribution    :   1.030

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 : 3.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.691
  Bond angles                    :   1.122
  Omega angle restraints         :   0.513 (tight)
  Side chain planarity           :   1.112
  Improper dihedral distribution :   1.250
  B-factor distribution          :   0.552
  Inside/Outside distribution    :   1.030
==============

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.