WHAT IF Check report

This file was created 2013-12-10 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 pdb4kd8.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: C 1 2 1
Number of matrices in space group: 4
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: 4
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: 865006.250
Volume of the Unit Cell V= 71992768.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 41.614
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.600 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

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.

4672 KBE   (   1-)  U  -
4673 DPP   (   2-)  U  -
4674 UAL   (   5-)  U  -
4675 5OH   (   6-)  U  -
4676 FUA   ( 701-)  Y  -
4677 GDP   ( 702-)  Y  -

Administrative problems that can generate validation failures

Warning: Amino acids observed inside ligands

Ligands were detected that contain amino acids. This is not a wise thing to do. Please rename those ligand fragments and call them DRG, XXX, or whatever, but do not give them the name of a valid amino acid, nucleotide, or sugar.

Crystallographers and NMR spectroscopists have an understandable dislike for organic chemistry and quantum chemistry. And they hate making topology entries for small molecules. So, if they find a funny small molecular ligand in their molecule, they generally try to 'recycle' old topologies. If the ligand contains a group that, for example, looks like an amino acid, it is common practice to split the ligand into several 'ligand-residues' and use the amino acid topology for the amino acid fragment. This is all fine, but please change the name into DRG, XXX, or whatever, before depositing the ligand. If you think that the validation software makes errors that are related to these ligands, I suggest you first change the name of the ligand (and make one ligand out of the fragments) and run the validation again. The table lists the residues, or residue-like things, that are found bound between ligands or unrecognized things, and that thus are suspect of actually being part of one big ligand.

4649 SER   (   3-)  U  -

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

4649 SER   (   3-)  U  -   N   bound to 4673 DPP   (   2-)  U  -   C

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: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: Y

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

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.

   3 GLU   (   9-)  B    High
   6 GLU   (  12-)  B    High
  10 HIS   (  16-)  B    High
  11 PHE   (  17-)  B    High
  27 TYR   (  33-)  B    High
  30 ARG   (  36-)  B    High
  42 MET   (  48-)  B    High
  44 GLU   (  50-)  B    High
  46 GLU   (  52-)  B    High
  50 ARG   (  56-)  B    High
  53 GLU   (  59-)  B    High
  54 ASP   (  60-)  B    High
  57 MET   (  63-)  B    High
  59 GLY   (  65-)  B    High
  70 GLN   (  76-)  B    High
  72 GLN   (  78-)  B    High
  78 GLU   (  84-)  B    High
  79 ALA   (  85-)  B    High
  84 MET   (  90-)  B    High
  93 GLY   (  99-)  B    High
  95 MET   ( 101-)  B    High
 118 SER   ( 124-)  B    High
 121 ILE   ( 127-)  B    High
 122 GLU   ( 128-)  B    High
 126 LYS   ( 132-)  B    High
And so on for a total of 1053 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: Y

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.

 444 ARG   (   3-)  D
 559 ARG   ( 118-)  D
2353 ARG   (  89-)  T
4016 ARG   (  38-)  Y
4309 ARG   ( 351-)  Y
4312 ARG   ( 354-)  Y
4315 ARG   ( 357-)  Y
4354 ARG   ( 396-)  Y
4442 ARG   ( 484-)  Y
4462 ARG   ( 504-)  Y
4477 ARG   ( 519-)  Y
4565 ARG   ( 607-)  Y
4618 ARG   ( 660-)  Y

Warning: Tyrosine convention problem

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

  25 TYR   (  31-)  B
  27 TYR   (  33-)  B
 230 TYR   ( 236-)  B
 435 TYR   ( 201-)  C
 461 TYR   (  20-)  D
 468 TYR   (  27-)  D
 479 TYR   (  38-)  D
 495 TYR   (  54-)  D
 509 TYR   (  68-)  D
 648 TYR   ( 207-)  D
 779 TYR   ( 133-)  E
 805 TYR   (   4-)  F
 860 TYR   (  59-)  F
 864 TYR   (  63-)  F
 945 TYR   (  44-)  G
 986 TYR   (  85-)  G
1055 TYR   ( 154-)  G
1105 TYR   (  48-)  H
1119 TYR   (  62-)  H
1122 TYR   (  65-)  H
1199 TYR   (   5-)  I
1256 TYR   (  62-)  I
1308 TYR   ( 114-)  I
1319 TYR   ( 125-)  I
1461 TYR   (  50-)  K
1634 TYR   (  98-)  L
1656 TYR   ( 120-)  L
1685 TYR   (  21-)  M
1970 TYR   (  32-)  P
2053 TYR   (  32-)  Q
2250 TYR   (  61-)  S
4013 TYR   (  35-)  Y
4144 TYR   ( 186-)  Y
4146 TYR   ( 188-)  Y
4530 TYR   ( 572-)  Y
4574 TYR   ( 616-)  Y
4634 TYR   ( 676-)  Y

Warning: Phenylalanine convention problem

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

  11 PHE   (  17-)  B
  64 PHE   (  70-)  B
 146 PHE   ( 152-)  B
 157 PHE   ( 163-)  B
 175 PHE   ( 181-)  B
 520 PHE   (  79-)  D
 534 PHE   (  93-)  D
 674 PHE   (  28-)  E
 691 PHE   (  45-)  E
 861 PHE   (  60-)  F
1212 PHE   (  18-)  I
1231 PHE   (  37-)  I
1331 PHE   (  11-)  J
1826 PHE   (  37-)  N
1864 PHE   (  15-)  O
1867 PHE   (  18-)  O
1947 PHE   (   9-)  P
2018 PHE   (  80-)  P
2092 PHE   (  71-)  Q
2133 PHE   (  29-)  R
2147 PHE   (  43-)  R
2199 PHE   (  10-)  S
2263 PHE   (  74-)  S
4031 PHE   (  73-)  Y
4217 PHE   ( 259-)  Y
4272 PHE   ( 314-)  Y
4396 PHE   ( 438-)  Y
4428 PHE   ( 470-)  Y
4516 PHE   ( 558-)  Y

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.

  54 ASP   (  60-)  B
 160 ASP   ( 166-)  B
 187 ASP   ( 193-)  B
 192 ASP   ( 198-)  B
 199 ASP   ( 205-)  B
 251 ASP   (  17-)  C
 270 ASP   (  36-)  C
 417 ASP   ( 183-)  C
 575 ASP   ( 134-)  D
 871 ASP   (  70-)  F
 884 ASP   (  83-)  F
 916 ASP   (  15-)  G
 946 ASP   (  45-)  G
1027 ASP   ( 126-)  G
1082 ASP   (  25-)  H
1109 ASP   (  52-)  H
1254 ASP   (  60-)  I
1269 ASP   (  75-)  I
1332 ASP   (  12-)  J
1445 ASP   (  34-)  K
1447 ASP   (  36-)  K
1522 ASP   ( 111-)  K
1648 ASP   ( 112-)  L
1711 ASP   (  47-)  M
1870 ASP   (  21-)  O
1923 ASP   (  74-)  O
1967 ASP   (  29-)  P
1978 ASP   (  40-)  P
1985 ASP   (  47-)  P
1990 ASP   (  52-)  P
2067 ASP   (  46-)  Q
2137 ASP   (  33-)  R
2201 ASP   (  12-)  S
2202 ASP   (  13-)  S
2328 ASP   (  64-)  T
4034 ASP   (  76-)  Y
4047 ASP   (  89-)  Y
4130 ASP   ( 172-)  Y
4153 ASP   ( 195-)  Y
4180 ASP   ( 222-)  Y
4182 ASP   ( 224-)  Y
4243 ASP   ( 285-)  Y
4331 ASP   ( 373-)  Y
4345 ASP   ( 387-)  Y
4378 ASP   ( 420-)  Y
4431 ASP   ( 473-)  Y
4520 ASP   ( 562-)  Y
4534 ASP   ( 576-)  Y
4616 ASP   ( 658-)  Y
4632 ASP   ( 674-)  Y

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.

   3 GLU   (   9-)  B
  14 GLU   (  20-)  B
  46 GLU   (  52-)  B
  53 GLU   (  59-)  B
 110 GLU   ( 116-)  B
 123 GLU   ( 129-)  B
 170 GLU   ( 176-)  B
 235 GLU   ( 241-)  B
 292 GLU   (  58-)  C
 316 GLU   (  82-)  C
 339 GLU   ( 105-)  C
 395 GLU   ( 161-)  C
 440 GLU   ( 206-)  C
 456 GLU   (  15-)  D
 513 GLU   (  72-)  D
 521 GLU   (  80-)  D
 522 GLU   (  81-)  D
 586 GLU   ( 145-)  D
 591 GLU   ( 150-)  D
 597 GLU   ( 156-)  D
 604 GLU   ( 163-)  D
 633 GLU   ( 192-)  D
 729 GLU   (  83-)  E
 768 GLU   ( 122-)  E
 823 GLU   (  22-)  F
And so on for a total of 81 lines.

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.

4465 TYR   ( 507-)  Y      N   -C     1.21   -6.0

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

 |  0.999681 -0.000035  0.000067|
 | -0.000035  0.999881 -0.000056|
 |  0.000067 -0.000056  0.999923|
Proposed new scale matrix

 |  0.003238  0.000000  0.000143|
 |  0.000000  0.001491  0.000000|
 |  0.000000  0.000000  0.002878|
With corresponding cell

    A    = 308.831  B   = 670.611  C    = 347.775
    Alpha=  90.006  Beta=  92.527  Gamma=  90.006

The CRYST1 cell dimensions

    A    = 308.961  B   = 670.662  C    = 347.765
    Alpha=  90.000  Beta=  92.520  Gamma=  90.000

Variance: 35.669
(Under-)estimated Z-score: 4.402

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.

  63 LEU   (  69-)  B     -C    N    CA  112.20   -5.3
 156 ILE   ( 162-)  B     -C    N    CA  110.54   -6.2
 156 ILE   ( 162-)  B      C    CA   CB  117.99    4.2
 157 PHE   ( 163-)  B      N    CA   C    91.55   -7.0
 158 VAL   ( 164-)  B     -O   -C    N   129.40    4.0
 158 VAL   ( 164-)  B     -C    N    CA  129.95    4.6
 166 ILE   ( 172-)  B      N    CA   C    99.72   -4.1
 179 ILE   ( 185-)  B      N    CA   C    99.24   -4.3
 180 ALA   ( 186-)  B     -C    N    CA  129.71    4.4
1569 ARG   (  33-)  L     -C    N    CA  114.46   -4.0
1571 GLY   (  35-)  L      N    CA   C   125.25    4.4
1591 VAL   (  55-)  L      C    CA   CB  101.08   -4.7
1606 ILE   (  70-)  L      C    CA   CB  102.24   -4.1
2081 ILE   (  60-)  Q     -C    N    CA  113.52   -4.5
2259 LYS   (  70-)  S      N    CA   C   122.66    4.1
2372 OGUA  (   6-)  A      N9   C8   N7  113.81    5.4
2373 OGUA  (   7-)  A      N9   C8   N7  113.21    4.2
2375 OGUA  (   9-)  A      N9   C8   N7  113.79    5.4
2377 OGUA  (  11-)  A      N9   C8   N7  113.30    4.4
2381 OGUA  (  15-)  A      N9   C4   N3  128.71    4.5
2387 OGUA  (  21-)  A      N9   C8   N7  113.33    4.5
2388 OGUA  (  22-)  A      N9   C8   N7  113.61    5.0
2395 OGUA  (  29-)  A      N9   C8   N7  113.65    5.1
2397 OGUA  (  31-)  A      N9   C8   N7  113.55    4.9
2398 OADE  (  32-)  A      C6   N1   C2  115.86   -4.6
And so on for a total of 516 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.

   3 GLU   (   9-)  B
  14 GLU   (  20-)  B
  46 GLU   (  52-)  B
  53 GLU   (  59-)  B
  54 ASP   (  60-)  B
 110 GLU   ( 116-)  B
 123 GLU   ( 129-)  B
 160 ASP   ( 166-)  B
 170 GLU   ( 176-)  B
 187 ASP   ( 193-)  B
 192 ASP   ( 198-)  B
 199 ASP   ( 205-)  B
 235 GLU   ( 241-)  B
 251 ASP   (  17-)  C
 270 ASP   (  36-)  C
 292 GLU   (  58-)  C
 316 GLU   (  82-)  C
 339 GLU   ( 105-)  C
 395 GLU   ( 161-)  C
 417 ASP   ( 183-)  C
 440 GLU   ( 206-)  C
 444 ARG   (   3-)  D
 456 GLU   (  15-)  D
 513 GLU   (  72-)  D
 521 GLU   (  80-)  D
And so on for a total of 144 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.

4460 GLY   ( 502-)  Y      C     -8.9   -11.73     0.06
4461 GLY   ( 503-)  Y      C      8.4    11.10     0.06
The average deviation= 0.666

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.

 157 PHE   ( 163-)  B    7.59
 166 ILE   ( 172-)  B    7.39
1571 GLY   (  35-)  L    6.03
1569 ARG   (  33-)  L    5.76
2081 ILE   (  60-)  Q    5.61
 347 ALA   ( 113-)  C    5.32
1497 GLY   (  86-)  K    5.08
 163 LYS   ( 169-)  B    5.05
1731 GLU   (  67-)  M    4.55
4525 LEU   ( 567-)  Y    4.51
4003 LYS   (  25-)  Y    4.42
4579 ILE   ( 621-)  Y    4.39
 181 LEU   ( 187-)  B    4.38
2259 LYS   (  70-)  S    4.36
2055 LYS   (  34-)  Q    4.32
   3 GLU   (   9-)  B    4.24
4090 ARG   ( 132-)  Y    4.23
   9 VAL   (  15-)  B    4.19
 179 ILE   ( 185-)  B    4.18
 182 ALA   ( 188-)  B    4.06

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.737

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.

 530 THR   (  89-)  D    -3.7
  97 THR   ( 103-)  B    -3.6
4444 THR   ( 486-)  Y    -3.6
1603 THR   (  67-)  L    -3.5
1578 THR   (  42-)  L    -3.5
  11 PHE   (  17-)  B    -3.5
1597 THR   (  61-)  L    -3.4
4045 HIS   (  87-)  Y    -3.4
1616 HIS   (  80-)  L    -3.3
2053 TYR   (  32-)  Q    -3.3
1960 THR   (  22-)  P    -3.2
4524 THR   ( 566-)  Y    -3.2
4446 THR   ( 488-)  Y    -3.2
1567 PRO   (  31-)  L    -3.1
4353 PRO   ( 395-)  Y    -3.1
1584 PRO   (  48-)  L    -3.1
1868 PRO   (  19-)  O    -3.0
4289 TYR   ( 331-)  Y    -3.0
 408 PRO   ( 174-)  C    -3.0
4498 PRO   ( 540-)  Y    -3.0
2248 PRO   (  59-)  S    -3.0
2266 THR   (  77-)  S    -3.0
 196 PRO   ( 202-)  B    -2.9
4363 PRO   ( 405-)  Y    -2.9
1606 ILE   (  70-)  L    -2.9
And so on for a total of 342 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 LYS   (   8-)  B  Poor phi/psi
   9 VAL   (  15-)  B  Poor phi/psi
  11 PHE   (  17-)  B  Poor phi/psi
  13 HIS   (  19-)  B  Poor phi/psi
  14 GLU   (  20-)  B  Poor phi/psi
  16 LYS   (  22-)  B  Poor phi/psi
  26 ILE   (  32-)  B  omega poor
  28 ALA   (  34-)  B  Poor phi/psi
  31 ASN   (  37-)  B  Poor phi/psi
  61 THR   (  67-)  B  Poor phi/psi
  62 ILE   (  68-)  B  omega poor
  70 GLN   (  76-)  B  Poor phi/psi
  88 ASN   (  94-)  B  Poor phi/psi
  89 GLN   (  95-)  B  Poor phi/psi
  94 GLY   ( 100-)  B  Poor phi/psi
  98 ASN   ( 104-)  B  Poor phi/psi
 119 PRO   ( 125-)  B  Poor phi/psi
 122 GLU   ( 128-)  B  Poor phi/psi
 123 GLU   ( 129-)  B  Poor phi/psi
 124 ARG   ( 130-)  B  Poor phi/psi
 151 ARG   ( 157-)  B  Poor phi/psi
 155 ALA   ( 161-)  B  Poor phi/psi
 156 ILE   ( 162-)  B  omega poor
 157 PHE   ( 163-)  B  omega poor
 158 VAL   ( 164-)  B  Poor phi/psi
And so on for a total of 476 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 : -6.008

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.

2301 SER   (  37-)  T    0.36
  75 VAL   (  81-)  B    0.38
1265 SER   (  71-)  I    0.38
2346 SER   (  82-)  T    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!

   9 VAL   (  15-)  B      0
  10 HIS   (  16-)  B      0
  11 PHE   (  17-)  B      0
  13 HIS   (  19-)  B      0
  14 GLU   (  20-)  B      0
  15 ARG   (  21-)  B      0
  16 LYS   (  22-)  B      0
  17 ARG   (  23-)  B      0
  18 TRP   (  24-)  B      0
  25 TYR   (  31-)  B      0
  28 ALA   (  34-)  B      0
  29 GLU   (  35-)  B      0
  30 ARG   (  36-)  B      0
  31 ASN   (  37-)  B      0
  38 LEU   (  44-)  B      0
  58 ARG   (  64-)  B      0
  61 THR   (  67-)  B      0
  64 PHE   (  70-)  B      0
  67 THR   (  73-)  B      0
  82 ALA   (  88-)  B      0
  84 MET   (  90-)  B      0
  88 ASN   (  94-)  B      0
  89 GLN   (  95-)  B      0
  90 ARG   (  96-)  B      0
  95 MET   ( 101-)  B      0
And so on for a total of 3022 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!

1657 GLY   ( 121-)  L   2.82   36
 681 GLY   (  35-)  E   2.65   11
1624 GLY   (  88-)  L   2.65   10
 259 GLY   (  25-)  C   2.64   14
1702 GLY   (  38-)  M   2.11   77
2001 GLY   (  63-)  P   1.95   17
4305 GLY   ( 347-)  Y   1.93   67
1216 GLY   (  22-)  I   1.79   14
2075 GLY   (  54-)  Q   1.79   80
4219 GLY   ( 261-)  Y   1.77   38
 197 GLY   ( 203-)  B   1.76   14
  32 GLY   (  38-)  B   1.70   51
1745 LEU   (  81-)  M   1.67   33
1251 GLY   (  57-)  I   1.61   29
1948 GLY   (  10-)  P   1.61   10
1356 GLY   (  36-)  J   1.53   27
1246 ALA   (  52-)  I   1.52   19
1100 GLY   (  43-)  H   1.50   36

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...

1569 ARG   (  33-)  L   1.99

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].

  20 PRO   (  26-)  B   102.5 envelop C-beta (108 degrees)
 125 PRO   ( 131-)  B    51.7 half-chair C-delta/C-gamma (54 degrees)
 153 PRO   ( 159-)  B    44.5 envelop C-delta (36 degrees)
 188 PRO   ( 194-)  B  -115.1 envelop C-gamma (-108 degrees)
 196 PRO   ( 202-)  B   -61.7 half-chair C-beta/C-alpha (-54 degrees)
 307 PRO   (  73-)  C   -53.8 half-chair C-beta/C-alpha (-54 degrees)
 348 PRO   ( 114-)  C   100.9 envelop C-beta (108 degrees)
 408 PRO   ( 174-)  C   -57.4 half-chair C-beta/C-alpha (-54 degrees)
 478 PRO   (  37-)  D   -60.9 half-chair C-beta/C-alpha (-54 degrees)
 638 PRO   ( 197-)  D  -115.8 envelop C-gamma (-108 degrees)
 695 PRO   (  49-)  E   103.7 envelop C-beta (108 degrees)
 742 PRO   (  96-)  E   101.4 envelop C-beta (108 degrees)
 752 PRO   ( 106-)  E   112.2 envelop C-beta (108 degrees)
 852 PRO   (  51-)  F  -119.4 half-chair C-delta/C-gamma (-126 degrees)
 869 PRO   (  68-)  F   -21.9 half-chair C-alpha/N (-18 degrees)
 994 PRO   (  93-)  G  -113.6 envelop C-gamma (-108 degrees)
1084 PRO   (  27-)  H   110.3 envelop C-beta (108 degrees)
1146 PRO   (  89-)  H  -113.8 envelop C-gamma (-108 degrees)
1243 PRO   (  49-)  I  -119.9 half-chair C-delta/C-gamma (-126 degrees)
1361 PRO   (  41-)  J  -130.3 half-chair C-delta/C-gamma (-126 degrees)
1397 PRO   (  77-)  J   -65.1 envelop C-beta (-72 degrees)
1524 PRO   ( 113-)  K    99.2 envelop C-beta (108 degrees)
1526 PRO   ( 115-)  K   -62.0 half-chair C-beta/C-alpha (-54 degrees)
1567 PRO   (  31-)  L   -24.9 half-chair C-alpha/N (-18 degrees)
1584 PRO   (  48-)  L   -18.9 half-chair C-alpha/N (-18 degrees)
1630 PRO   (  94-)  L   100.9 envelop C-beta (108 degrees)
1661 PRO   ( 125-)  L   105.7 envelop C-beta (108 degrees)
1761 PRO   (  97-)  M  -122.3 half-chair C-delta/C-gamma (-126 degrees)
1788 PRO   ( 124-)  M   114.6 envelop C-beta (108 degrees)
1843 PRO   (  54-)  N    42.6 envelop C-delta (36 degrees)
1868 PRO   (  19-)  O   108.8 envelop C-beta (108 degrees)
1979 PRO   (  41-)  P  -112.4 envelop C-gamma (-108 degrees)
1984 PRO   (  46-)  P  -113.9 envelop C-gamma (-108 degrees)
2004 PRO   (  66-)  P   -63.8 envelop C-beta (-72 degrees)
2051 PRO   (  30-)  Q  -122.9 half-chair C-delta/C-gamma (-126 degrees)
2085 PRO   (  64-)  Q   107.9 envelop C-beta (108 degrees)
2231 PRO   (  42-)  S   121.8 half-chair C-beta/C-alpha (126 degrees)
2248 PRO   (  59-)  S   -48.6 half-chair C-beta/C-alpha (-54 degrees)
4074 PRO   ( 116-)  Y   -50.8 half-chair C-beta/C-alpha (-54 degrees)
4241 PRO   ( 283-)  Y    99.3 envelop C-beta (108 degrees)
4246 PRO   ( 288-)  Y   109.5 envelop C-beta (108 degrees)
4353 PRO   ( 395-)  Y   126.8 half-chair C-beta/C-alpha (126 degrees)
4394 PRO   ( 436-)  Y  -123.6 half-chair C-delta/C-gamma (-126 degrees)
4476 PRO   ( 518-)  Y   171.9 envelop N (180 degrees)
4498 PRO   ( 540-)  Y    35.5 envelop C-delta (36 degrees)
4517 PRO   ( 559-)  Y   103.5 envelop C-beta (108 degrees)
4594 PRO   ( 636-)  Y  -141.0 envelop C-delta (-144 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.

4672 KBE   (   1-)  U      C   <-> 4673 DPP   (   2-)  U      N      1.38    1.32  INTRA BL
4673 DPP   (   2-)  U      NG  <-> 4675 5OH   (   6-)  U      C      1.36    1.34  INTRA BL
4674 UAL   (   5-)  U      C   <-> 4675 5OH   (   6-)  U      N      1.34    1.36  INTRA BL
4649 SER   (   3-)  U      N   <-> 4673 DPP   (   2-)  U      C      1.32    1.38  INTRA BF
1813 CYS   (  24-)  N      CB  <-> 1829 CYS   (  40-)  N      SG     1.20    2.20  INTRA BL
3164 OADE  ( 815-)  A      N1  <-> 3851 OGUA  (1508-)  A      N2     1.07    1.93  INTRA BL
4673 DPP   (   2-)  U      CB  <-> 4675 5OH   (   6-)  U      C      0.74    2.46  INTRA BL
4649 SER   (   3-)  U      CA  <-> 4673 DPP   (   2-)  U      C      0.72    2.48  INTRA BF
 467 CYS   (  26-)  D      SG  <->  472 CYS   (  31-)  D      CA     0.70    2.70  INTRA BL
3896 OGUA  (  15-)  W      N1  <-> 3930 OCYT  (  48-)  W      N3     0.70    2.30  INTRA BF
3896 OGUA  (  15-)  W      N2  <-> 3930 OCYT  (  48-)  W      N4     0.69    2.16  INTRA BF
3761 OADE  (1413-)  A      N1  <-> 3830 OGUA  (1487-)  A      N2     0.68    2.32  INTRA BL
3164 OADE  ( 815-)  A      C2  <-> 3870 OCYT  (1527-)  A      O2     0.67    2.13  INTRA BL
2471 OGUA  ( 112-)  A      N2  <-> 2676 OADE  ( 315-)  A      N1     0.65    2.35  INTRA BF
2734 OADE  ( 373-)  A      N3  <-> 2831 OGUA  ( 481-)  A      N2     0.65    2.35  INTRA BF
3932 OCYT  (  50-)  W      N3  <-> 3946 OGUA  (  64-)  W      N2     0.62    2.38  INTRA BF
4672 KBE   (   1-)  U      CA  <-> 4673 DPP   (   2-)  U      N      0.60    2.40  INTRA BL
3899 OGUA  (  18-)  W      N2  <-> 3940 OADE  (  58-)  W      OP1    0.60    2.10  INTRA BF
3425 OGUA  (1077-)  A      N2  <-> 3428 OADE  (1080-)  A      OP2    0.59    2.11  INTRA BL
3413 OURA  (1065-)  A      O2  <-> 3415 OADE  (1067-)  A      N6     0.58    2.12  INTRA BL
4674 UAL   (   5-)  U      CA  <-> 4675 5OH   (   6-)  U      N      0.57    2.43  INTRA BL
3652 OGUA  (1305-)  A      N2  <-> 3679 OADE  (1332-)  A      N7     0.56    2.44  INTRA BF
3347 OGUA  (1003-)  A      N1  <-> 3385 OCYT  (1037-)  A      O2     0.55    2.15  INTRA BF
 198 ASN   ( 204-)  B      OD1 <->  201 ALA   ( 207-)  B      N      0.55    2.15  INTRA BF
1573 CYS   (  37-)  L      SG  <-> 1574 THR   (  38-)  L      N      0.55    2.65  INTRA BL
And so on for a total of 2200 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

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.

1937 ARG   (  88-)  O      -8.56
4279 TYR   ( 321-)  Y      -8.54
1436 TYR   (  25-)  K      -8.51
1789 ARG   ( 125-)  M      -8.35
 980 ARG   (  79-)  G      -8.23
2269 TYR   (  80-)  S      -8.22
 313 ARG   (  79-)  C      -8.08
 445 TYR   (   4-)  D      -7.95
 905 ARG   (   4-)  G      -7.95
1768 ARG   ( 104-)  M      -7.85
1015 ARG   ( 114-)  G      -7.82
 490 ARG   (  49-)  D      -7.73
1763 ARG   (  99-)  M      -7.73
1531 ARG   ( 120-)  K      -7.70
 772 ARG   ( 126-)  E      -7.53
2270 ARG   (  81-)  S      -7.43
 483 GLN   (  42-)  D      -7.42
1371 ARG   (  51-)  J      -7.20
 907 ARG   (   6-)  G      -7.16
1308 TYR   ( 114-)  I      -7.13
2363 LEU   (  99-)  T      -7.10
1151 TYR   (  94-)  H      -7.09
1319 TYR   ( 125-)  I      -7.05
1625 ARG   (  89-)  L      -7.02
4586 ARG   ( 628-)  Y      -7.01
And so on for a total of 218 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.

  15 ARG   (  21-)  B        17 - ARG     23- ( B)         -4.88
 236 GLY   (   2-)  C       239 - ILE      5- ( C)         -4.90
 444 ARG   (   3-)  D       446 - ILE      5- ( D)         -6.40
 486 GLN   (  45-)  D       488 - ARG     47- ( D)         -5.42
 525 LYS   (  84-)  D       527 - LYS     86- ( D)         -5.62
 665 MET   (  19-)  E       668 - GLY     22- ( E)         -4.63
 717 LEU   (  71-)  E       719 - ASN     73- ( E)         -5.09
 846 LEU   (  45-)  F       848 - ARG     47- ( F)         -5.23
 904 ARG   (   3-)  G       907 - ARG      6- ( G)         -7.07
 909 GLU   (   8-)  G       913 - LEU     12- ( G)         -5.07
 952 GLN   (  51-)  G       954 - LYS     53- ( G)         -4.32
1125 ARG   (  68-)  H      1127 - GLN     70- ( H)         -5.77
1154 VAL   (  97-)  H      1156 - GLU     99- ( H)         -4.58
1161 ARG   ( 104-)  H      1164 - LEU    107- ( H)         -4.73
1374 PHE   (  54-)  J      1377 - LYS     57- ( J)         -5.53
1422 LYS   (  11-)  K      1425 - VAL     14- ( K)         -4.70
1527 HIS   ( 116-)  K      1531 - ARG    120- ( K)         -5.93
1554 VAL   (  18-)  L      1557 - LYS     21- ( L)         -5.66
1588 LEU   (  52-)  L      1590 - LYS     54- ( L)         -4.26
1778 ARG   ( 114-)  M      1781 - VAL    117- ( M)         -5.17
1784 LYS   ( 120-)  M      1786 - LYS    122- ( M)         -6.43
1946 ARG   (   8-)  P      1948 - GLY     10- ( P)         -4.63
1950 LYS   (  12-)  P      1952 - ASN     14- ( P)         -5.50
1980 ARG   (  42-)  P      1982 - THR     44- ( P)         -5.09
2018 PHE   (  80-)  P      2021 - GLU     83- ( P)         -5.42
2194 LEU   (   5-)  S      2196 - LYS      7- ( S)         -5.86
2267 ARG   (  78-)  S      2271 - GLY     82- ( S)         -6.16
2368 LEU   ( 104-)  T      2370 - ALA    106- ( T)         -4.37
3998 HIS   (  20-)  Y      4000 - ASP     22- ( Y)         -4.20
4016 ARG   (  38-)  Y      4021 - GLY     43- ( Y)         -5.18
4457 ARG   ( 499-)  Y      4459 - THR    501- ( Y)         -5.51

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 4650 : -1.730

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: Y

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.

 483 GLN   (  42-)  D   -3.52
2088 LYS   (  67-)  Q   -3.33
1375 LYS   (  55-)  J   -3.23
1437 ASN   (  26-)  K   -3.21
1582 LYS   (  46-)  L   -3.21
1789 ARG   ( 125-)  M   -3.20
1768 ARG   ( 104-)  M   -3.19
 237 ASN   (   3-)  C   -3.18
1770 ASN   ( 106-)  M   -3.16
 668 GLY   (  22-)  E   -3.09
1820 ARG   (  31-)  N   -3.08
1374 PHE   (  54-)  J   -3.07
 444 ARG   (   3-)  D   -3.07
 474 MET   (  33-)  D   -3.05
 905 ARG   (   4-)  G   -3.03
1321 LYS   ( 127-)  I   -3.02
1058 MET   (   1-)  H   -2.99
1312 LYS   ( 118-)  I   -2.98
2243 GLY   (  54-)  S   -2.96
1529 GLY   ( 118-)  K   -2.96
2195 LYS   (   6-)  S   -2.93
1527 HIS   ( 116-)  K   -2.88
2274 LEU   (  10-)  T   -2.88
1585 ASN   (  49-)  L   -2.88
1306 LYS   ( 112-)  I   -2.86
And so on for a total of 62 lines.

Warning: Abnormal packing Z-score for sequential residues

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

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

 236 GLY   (   2-)  C     -  239 ILE   (   5-)  C        -2.43
 481 PRO   (  40-)  D     -  484 HIS   (  43-)  D        -2.16
 903 ALA   (   2-)  G     -  906 ARG   (   5-)  G        -2.32
 932 MET   (  31-)  G     -  937 LYS   (  36-)  G        -2.10
1057 TRP   ( 156-)  G     - 1060 THR   (   3-)  H        -2.13
1304 GLU   ( 110-)  I     - 1308 TYR   ( 114-)  I        -2.10
1317 PRO   ( 123-)  I     - 1322 ARG   ( 128-)  I        -2.49
1358 ILE   (  38-)  J     - 1361 PRO   (  41-)  J        -1.79
1373 PRO   (  53-)  J     - 1378 ASP   (  58-)  J        -2.37
1408 LEU   (  88-)  J     - 1411 PRO   (  91-)  J        -1.87
1526 PRO   ( 115-)  K     - 1531 ARG   ( 120-)  K        -2.15
1580 THR   (  44-)  L     - 1585 ASN   (  49-)  L        -2.20
1761 PRO   (  97-)  M     - 1766 ARG   ( 102-)  M        -2.07
1804 LYS   (  15-)  N     - 1808 ARG   (  19-)  N        -1.86
1846 ARG   (  57-)  N     - 1849 SER   (  60-)  N        -1.94
1964 ARG   (  26-)  P     - 1969 LYS   (  31-)  P        -2.07
2034 ASP   (  13-)  Q     - 2037 GLN   (  16-)  Q        -1.87
2057 ILE   (  36-)  Q     - 2060 SER   (  39-)  Q        -1.69
2082 GLU   (  61-)  Q     - 2085 PRO   (  64-)  Q        -1.92

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: Y

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.

  72 GLN   (  78-)  B
 140 GLN   ( 146-)  B
 373 GLN   ( 139-)  C
 518 ASN   (  77-)  D
 544 ASN   ( 103-)  D
 557 GLN   ( 116-)  D
 560 GLN   ( 119-)  D
 642 GLN   ( 201-)  D
 711 ASN   (  65-)  E
 814 ASN   (  13-)  F
 938 ASN   (  37-)  G
 965 GLN   (  64-)  G
 985 ASN   (  84-)  G
1138 HIS   (  81-)  H
1197 GLN   (   3-)  I
1267 GLN   (  73-)  I
1281 GLN   (  87-)  I
1433 HIS   (  22-)  K
1527 HIS   ( 116-)  K
1544 ASN   (   8-)  L
1756 HIS   (  92-)  M
1765 GLN   ( 101-)  M
2037 GLN   (  16-)  Q
2114 GLN   (  93-)  Q
2212 ASN   (  23-)  S
3992 ASN   (  14-)  Y
4095 ASN   ( 137-)  Y
4485 ASN   ( 527-)  Y

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.

  12 GLY   (  18-)  B      N
  13 HIS   (  19-)  B      N
  16 LYS   (  22-)  B      N
  29 GLU   (  35-)  B      N
  30 ARG   (  36-)  B      N
  34 HIS   (  40-)  B      NE2
  36 ILE   (  42-)  B      N
  48 THR   (  54-)  B      OG1
  65 VAL   (  71-)  B      N
  70 GLN   (  76-)  B      N
  71 ALA   (  77-)  B      N
  81 ARG   (  87-)  B      NH1
  86 TYR   (  92-)  B      N
  89 GLN   (  95-)  B      N
  90 ARG   (  96-)  B      N
  91 TRP   (  97-)  B      NE1
  94 GLY   ( 100-)  B      N
  95 MET   ( 101-)  B      N
  96 LEU   ( 102-)  B      N
  99 PHE   ( 105-)  B      N
 100 LYS   ( 106-)  B      N
 117 ALA   ( 123-)  B      N
 121 ILE   ( 127-)  B      N
 123 GLU   ( 129-)  B      N
 127 LYS   ( 133-)  B      N
And so on for a total of 751 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.

  10 HIS   (  16-)  B      ND1
  44 GLU   (  50-)  B      OE1
  78 GLU   (  84-)  B      OE2
 135 GLU   ( 141-)  B      OE1
 135 GLU   ( 141-)  B      OE2
 160 ASP   ( 166-)  B      OD1
 170 GLU   ( 176-)  B      OE2
 198 ASN   ( 204-)  B      OD1
 206 GLN   ( 212-)  B      OE1
 270 ASP   (  36-)  C      OD1
 359 GLU   ( 125-)  C      OE1
 564 HIS   ( 123-)  D      ND1
 641 GLU   ( 200-)  D      OE1
 912 GLN   (  11-)  G      OE1
1024 GLU   ( 123-)  G      OE2
1065 ASP   (   8-)  H      OD1
1065 ASP   (   8-)  H      OD2
1072 ASN   (  15-)  H      OD1
1135 GLN   (  78-)  H      OE1
1267 GLN   (  73-)  I      OE1
1382 HIS   (  62-)  J      ND1
1384 GLU   (  64-)  J      OE1
1393 ASP   (  73-)  J      OD1
1611 HIS   (  75-)  L      ND1
1615 GLU   (  79-)  L      OE2
1628 ASP   (  92-)  L      OD1
1680 ASP   (  16-)  M      OD1
1747 ASP   (  83-)  M      OD2
1838 HIS   (  49-)  N      ND1
2066 HIS   (  45-)  Q      ND1
2067 ASP   (  46-)  Q      OD1
2070 GLU   (  49-)  Q      OE2
2134 ASP   (  30-)  R      OD1
2242 ASN   (  53-)  S      OD1
2324 GLU   (  60-)  T      OE2
2328 ASP   (  64-)  T      OD1
3992 ASN   (  14-)  Y      OD1
4073 GLU   ( 115-)  Y      OE2
4077 GLU   ( 119-)  Y      OE1
4077 GLU   ( 119-)  Y      OE2
4123 GLN   ( 165-)  Y      OE1
4148 ASN   ( 190-)  Y      OD1
4182 ASP   ( 224-)  Y      OD1
4199 GLU   ( 241-)  Y      OE2
4326 GLU   ( 368-)  Y      OE1
4380 GLU   ( 422-)  Y      OE1
4599 GLN   ( 641-)  Y      OE1
4635 GLN   ( 677-)  Y      OE1

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+.

4671  MG   ( 703-)  Y   -.-  -.-  Too few ligands (0)
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.

   6 GLU   (  12-)  B   H-bonding suggests Gln
  43 GLU   (  49-)  B   H-bonding suggests Gln
  44 GLU   (  50-)  B   H-bonding suggests Gln
  46 GLU   (  52-)  B   H-bonding suggests Gln
  54 ASP   (  60-)  B   H-bonding suggests Asn
 110 GLU   ( 116-)  B   H-bonding suggests Gln; but Alt-Rotamer
 111 GLU   ( 117-)  B   H-bonding suggests Gln
 120 GLU   ( 126-)  B   H-bonding suggests Gln; but Alt-Rotamer
 135 GLU   ( 141-)  B   H-bonding suggests Gln
 154 ASP   ( 160-)  B   H-bonding suggests Asn
 164 GLU   ( 170-)  B   H-bonding suggests Gln; but Alt-Rotamer
 170 GLU   ( 176-)  B   H-bonding suggests Gln
 192 ASP   ( 198-)  B   H-bonding suggests Asn
 214 ASP   ( 220-)  B   H-bonding suggests Asn; but Alt-Rotamer
 251 ASP   (  17-)  C   H-bonding suggests Asn
 290 ASP   (  56-)  C   H-bonding suggests Asn
 359 GLU   ( 125-)  C   H-bonding suggests Gln
 513 GLU   (  72-)  D   H-bonding suggests Gln
 634 ASP   ( 193-)  D   H-bonding suggests Asn; but Alt-Rotamer
 654 GLU   (   8-)  E   H-bonding suggests Gln
 682 ASP   (  36-)  E   H-bonding suggests Asn; but Alt-Rotamer
 763 ASP   ( 117-)  E   H-bonding suggests Asn
 768 GLU   ( 122-)  E   H-bonding suggests Gln
 783 GLU   ( 137-)  E   H-bonding suggests Gln; but Alt-Rotamer
 806 GLU   (   5-)  F   H-bonding suggests Gln
And so on for a total of 77 lines.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -3.075
  2nd generation packing quality :  -3.924 (poor)
  Ramachandran plot appearance   :  -5.737 (bad)
  chi-1/chi-2 rotamer normality  :  -6.008 (bad)
  Backbone conformation          :  -1.183

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.486 (tight)
  Bond angles                    :   0.919
  Omega angle restraints         :   1.104
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.491
  Inside/Outside distribution    :   1.037

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 : 3.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.6
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -2.6
  chi-1/chi-2 rotamer normality  :  -3.4 (poor)
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.486 (tight)
  Bond angles                    :   0.919
  Omega angle restraints         :   1.104
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.491
  Inside/Outside distribution    :   1.037
==============

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.