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 pdb4k0m.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 21 21 21
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: 1347176.3
Volume of the Unit Cell V= 59015868.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 21.904
Vm by authors and this calculated Vm do not agree very well
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

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

3926 GLY   ( 129-)  G  -
5813 CYS   (  79-)  Y  -

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: 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: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: 0

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Note: Ramachandran plot

Chain identifier: 9

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

Warning: Artificial side chains detected

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

2928 VAL   (  19-)  C
5055 VAL   (  97-)  R

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 OADE  (   5-)  A    High
   2 OGUA  (   6-)  A    High
   3 OADE  (   7-)  A    High
   4 OURA  (   8-)  A    High
   5 OGUA  (   9-)  A    High
   6 OGUA  (  10-)  A    High
   7 OURA  (  11-)  A    High
  29 OCYT  (  33-)  A    High
  84 OURA  (  88-)  A    High
  85 OADE  (  89-)  A    High
  86 OGUA  (  90-)  A    High
  94 OGUA  (  98-)  A    High
 149 OGUA  ( 153-)  A    High
 150 OCYT  ( 154-)  A    High
 151 OURA  ( 157-)  A    High
 152 OURA  ( 158-)  A    High
 153 OGUA  ( 159-)  A    High
 154 OCYT  ( 160-)  A    High
 155 OGUA  ( 161-)  A    High
 156 OCYT  ( 162-)  A    High
 210 OADE  ( 216-)  A    High
 211 OADE  ( 217-)  A    High
 212 OURA  ( 218-)  A    High
 257 OGUA  ( 263-)  A    High
 258 OURA  ( 264-)  A    High
And so on for a total of 1243 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :277.000

Note: B-factor plot

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

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: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: 0

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: 4

Note: B-factor plot

Chain identifier: 5

Note: B-factor plot

Chain identifier: 6

Note: B-factor plot

Chain identifier: 7

Note: B-factor plot

Chain identifier: 8

Note: B-factor plot

Chain identifier: 9

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.

3354 ARG   ( 239-)  D
3445 ARG   (  58-)  E
4709 ARG   (  41-)  P
4718 ARG   (  50-)  P
4723 ARG   (  55-)  P
4770 ARG   ( 102-)  P
4779 ARG   ( 111-)  P
5022 ARG   (  64-)  R
5046 ARG   (  88-)  R
5360 ARG   (  50-)  U
5374 ARG   (  64-)  U
6040 ARG   (  32-)  0
6143 ARG   (  52-)  1
6240 ARG   (  55-)  2

Warning: Tyrosine convention problem

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

3219 TYR   ( 104-)  D
3287 TYR   ( 172-)  D
3547 TYR   ( 160-)  E
3650 TYR   (  59-)  F
3688 TYR   (  97-)  F
3690 TYR   (  99-)  F
3809 TYR   (  12-)  G
4050 TYR   (  83-)  H
4131 TYR   ( 164-)  H
4162 TYR   (  25-)  I
4226 TYR   (  89-)  I
4263 TYR   ( 126-)  I
4484 TYR   (  72-)  N
4582 TYR   (  32-)  O
4748 TYR   (  80-)  P
4827 TYR   (   9-)  Q
4955 TYR   ( 137-)  Q
4979 TYR   (  21-)  R
5052 TYR   (  94-)  R
5160 TYR   (  94-)  S
5242 TYR   (  68-)  T
5274 TYR   ( 100-)  T
5334 TYR   (  24-)  U
5355 TYR   (  45-)  U
5357 TYR   (  47-)  U
5386 TYR   (  76-)  U
5440 TYR   (  12-)  V
5509 TYR   (  81-)  V
5538 TYR   (   9-)  W
5599 TYR   (  70-)  W
5604 TYR   (  75-)  W
5645 TYR   (   5-)  X
5709 TYR   (  69-)  X
5768 TYR   (  35-)  Y
5788 TYR   (  55-)  Y
5834 TYR   (   3-)  Z
5840 TYR   (   9-)  Z
5930 TYR   (  99-)  Z
6034 TYR   (  26-)  0
6134 TYR   (  43-)  1
6332 TYR   (  51-)  4
6339 TYR   (  58-)  4
6418 TYR   (  21-)  6

Warning: Phenylalanine convention problem

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

2940 PHE   (  37-)  C
3130 PHE   (  15-)  D
3136 PHE   (  21-)  D
3182 PHE   (  67-)  D
3250 PHE   ( 135-)  D
3438 PHE   (  51-)  E
3471 PHE   (  84-)  E
3500 PHE   ( 113-)  E
3674 PHE   (  83-)  F
3820 PHE   (  23-)  G
3899 PHE   ( 102-)  G
3937 PHE   ( 141-)  G
4090 PHE   ( 123-)  H
4798 PHE   ( 130-)  P
4883 PHE   (  65-)  Q
5038 PHE   (  80-)  R
5078 PHE   (  12-)  S
5095 PHE   (  29-)  S
5196 PHE   (  22-)  T
5219 PHE   (  45-)  T
5231 PHE   (  57-)  T
5235 PHE   (  61-)  T
5250 PHE   (  76-)  T
5350 PHE   (  40-)  U
5389 PHE   (  79-)  U
5430 PHE   (   2-)  V
5661 PHE   (  21-)  X
5687 PHE   (  47-)  X
5793 PHE   (  60-)  Y
5875 PHE   (  44-)  Z
5919 PHE   (  88-)  Z
5920 PHE   (  89-)  Z
5967 PHE   ( 136-)  Z
6053 PHE   (  45-)  0
6068 PHE   (  60-)  0
6151 PHE   (  60-)  1
6467 PHE   (  18-)  7
6544 PHE   (  48-)  8

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.

2953 ASP   (  50-)  C
3214 ASP   (  99-)  D
3224 ASP   ( 109-)  D
3237 ASP   ( 122-)  D
3404 ASP   (  17-)  E
3470 ASP   (  83-)  E
3561 ASP   ( 174-)  E
3707 ASP   ( 116-)  F
3913 ASP   ( 116-)  G
4429 ASP   (  17-)  N
4562 ASP   (  12-)  O
4606 ASP   (  56-)  O
4673 ASP   (   5-)  P
5017 ASP   (  59-)  R
5027 ASP   (  69-)  R
5030 ASP   (  72-)  R
5065 ASP   ( 107-)  R
5108 ASP   (  42-)  S
5154 ASP   (  88-)  S
5200 ASP   (  26-)  T
5261 ASP   (  87-)  T
5551 ASP   (  22-)  W
5623 ASP   (  94-)  W
5876 ASP   (  45-)  Z
5985 ASP   ( 154-)  Z
6023 ASP   (  15-)  0
6064 ASP   (  56-)  0
6237 ASP   (  52-)  2

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.

3000 GLU   (  97-)  C
3138 GLU   (  23-)  D
3216 GLU   ( 101-)  D
3284 GLU   ( 169-)  D
3296 GLU   ( 181-)  D
3460 GLU   (  73-)  E
3481 GLU   (  94-)  E
3558 GLU   ( 171-)  E
3566 GLU   ( 179-)  E
3587 GLU   ( 200-)  E
3618 GLU   (  27-)  F
3626 GLU   (  35-)  F
3647 GLU   (  56-)  F
3781 GLU   ( 190-)  F
3810 GLU   (  13-)  G
3811 GLU   (  14-)  G
3933 GLU   ( 137-)  G
3970 GLU   ( 174-)  G
4053 GLU   (  86-)  H
4144 GLU   (   7-)  I
4197 GLU   (  60-)  I
4201 GLU   (  64-)  I
4254 GLU   ( 117-)  I
4480 GLU   (  68-)  N
4508 GLU   (  96-)  N
And so on for a total of 63 lines.

Warning: Phosphate group convention problem

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

 151 OURA  ( 157-)  A
 292 OCYT  ( 302-)  A
1062 OADE  (1151-)  A
1491 OCYT  (1589-)  A

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.

 792 OADE  ( 829-)  A      P    OP2   1.56    4.2
 952 OADE  ( 989-)  A      O4'  C1'   1.35   -5.3
2415 OGUA  (2513-)  A      P    OP2   1.56    4.6
3514 ASP   ( 127-)  E      CA   C     1.61    4.1
3514 ASP   ( 127-)  E      CB   CG    1.64    4.8
4124 TYR   ( 157-)  H      CB   CG    1.60    4.0
4691 PRO   (  23-)  P      CA   C     1.61    4.1
4707 LYS   (  39-)  P      CA   C     1.61    4.2
6445 VAL   (  48-)  6      N   -C     1.53    9.9

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

 |  1.000407 -0.000040  0.000036|
 | -0.000040  1.000534  0.000061|
 |  0.000036  0.000061  1.000098|
Proposed new scale matrix

 |  0.004762  0.000000  0.000000|
 |  0.000000  0.002222  0.000000|
 |  0.000000  0.000000  0.001600|
With corresponding cell

    A    = 209.993  B   = 450.083  C    = 625.062
    Alpha=  90.006  Beta=  90.005  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 209.908  B   = 449.843  C    = 625.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 218.702
(Under-)estimated Z-score: 10.899

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 OGUA  (   6-)  A      N9   C8   N7  113.14    4.1
   5 OGUA  (   9-)  A      N9   C8   N7  113.10    4.0
   6 OGUA  (  10-)  A      N9   C8   N7  113.18    4.2
  10 OGUA  (  14-)  A      N9   C8   N7  113.16    4.1
  19 OGUA  (  23-)  A      N9   C8   N7  113.15    4.1
  21 OGUA  (  25-)  A      N9   C8   N7  113.14    4.1
  25 OGUA  (  29-)  A      N9   C8   N7  113.19    4.2
  39 OGUA  (  43-)  A      N9   C8   N7  113.16    4.1
  44 OURA  (  48-)  A      P   -C3* -O3* 125.14    4.5
  45 OGUA  (  49-)  A      N9   C8   N7  113.16    4.1
  68 OADE  (  72-)  A      OP2  P    O5' 120.58    4.5
  75 OGUA  (  79-)  A      N9   C8   N7  113.13    4.1
  82 OGUA  (  86-)  A      N9   C8   N7  113.20    4.2
  94 OGUA  (  98-)  A      C2'  C1'  N9  121.03    4.8
  95 OGUA  (  99-)  A      C2'  C1'  N9  120.13    4.2
  95 OGUA  (  99-)  A      N9   C8   N7  113.14    4.1
 112 OADE  ( 116-)  A      C2'  C1'  N9  121.24    4.9
 115 OGUA  ( 119-)  A      N9   C8   N7  113.12    4.0
 121 OCYT  ( 125-)  A      O3'  C3'  C4' 123.18    4.8
 121 OCYT  ( 125-)  A      C4'  C3'  C2'  98.58   -4.1
 125 OGUA  ( 129-)  A      N9   C8   N7  113.15    4.1
 132 OGUA  ( 136-)  A      N9   C8   N7  113.25    4.3
 147 OGUA  ( 151-)  A      N9   C8   N7  113.12    4.0
 151 OURA  ( 157-)  A      OP2  P   -O3*  85.06   -7.3
 151 OURA  ( 157-)  A      O5*  P   -O3* 113.96    5.2
And so on for a total of 621 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.

2953 ASP   (  50-)  C
3000 GLU   (  97-)  C
3138 GLU   (  23-)  D
3214 ASP   (  99-)  D
3216 GLU   ( 101-)  D
3224 ASP   ( 109-)  D
3237 ASP   ( 122-)  D
3284 GLU   ( 169-)  D
3296 GLU   ( 181-)  D
3354 ARG   ( 239-)  D
3404 ASP   (  17-)  E
3445 ARG   (  58-)  E
3460 GLU   (  73-)  E
3470 ASP   (  83-)  E
3481 GLU   (  94-)  E
3558 GLU   ( 171-)  E
3561 ASP   ( 174-)  E
3566 GLU   ( 179-)  E
3587 GLU   ( 200-)  E
3618 GLU   (  27-)  F
3626 GLU   (  35-)  F
3647 GLU   (  56-)  F
3707 ASP   ( 116-)  F
3781 GLU   ( 190-)  F
3810 GLU   (  13-)  G
And so on for a total of 105 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.

4691 PRO   (  23-)  P      N     -8.5   -30.47    -2.48
The average deviation= 1.010

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.

4709 ARG   (  41-)  P    6.07
5368 ARG   (  58-)  U    5.68
4726 THR   (  58-)  P    5.57
6596 GLY   (  37-)  9    5.30
6442 LYS   (  45-)  6    5.22
3325 GLY   ( 210-)  D    5.20
6355 LYS   (  10-)  5    4.97
5204 VAL   (  30-)  T    4.92
5158 TYR   (  92-)  S    4.90
5402 ARG   (  92-)  U    4.85
5130 GLU   (  64-)  S    4.84
5684 GLU   (  44-)  X    4.63
5468 LEU   (  40-)  V    4.63
3339 ALA   ( 224-)  D    4.41
5203 ARG   (  29-)  T    4.40
6397 TYR   (  52-)  5    4.38
3186 ASP   (  71-)  D    4.37
4691 PRO   (  23-)  P    4.36
5323 LYS   (  13-)  U    4.34
6394 CYS   (  49-)  5    4.32
5096 ARG   (  30-)  S    4.26
5400 VAL   (  90-)  U    4.25
4723 ARG   (  55-)  P    4.21
3612 ALA   (  21-)  F    4.19
5089 ARG   (  23-)  S    4.18
6152 ARG   (  61-)  1    4.15
3156 GLY   (  41-)  D    4.15
6552 GLU   (  56-)  8    4.11
5239 LYS   (  65-)  T    4.06
3980 LYS   (  13-)  H    4.06
3360 PRO   ( 245-)  D    4.03
4479 LEU   (  67-)  N    4.00

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 : -5.100

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.

4124 TYR   ( 157-)  H    -3.7
4725 THR   (  57-)  P    -3.4
3142 THR   (  27-)  D    -3.2
5789 PRO   (  56-)  Y    -3.1
3473 PRO   (  86-)  E    -3.1
5810 PRO   (  77-)  Y    -3.1
5191 THR   (  17-)  T    -3.1
4598 PRO   (  48-)  O    -3.1
6428 PRO   (  31-)  6    -3.1
5198 PRO   (  24-)  T    -3.1
3356 PRO   ( 241-)  D    -3.1
4691 PRO   (  23-)  P    -3.1
3884 PRO   (  87-)  G    -3.0
4269 PRO   ( 132-)  I    -3.0
3616 PRO   (  25-)  F    -3.0
5765 PRO   (  32-)  Y    -3.0
4121 PRO   ( 154-)  H    -3.0
4416 TYR   (   4-)  N    -2.9
5457 PRO   (  29-)  V    -2.9
4731 PRO   (  63-)  P    -2.9
5446 LEU   (  18-)  V    -2.9
5799 PRO   (  66-)  Y    -2.9
3168 PHE   (  53-)  D    -2.8
4095 PRO   ( 128-)  H    -2.8
3469 ARG   (  82-)  E    -2.8
And so on for a total of 401 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.

2928 VAL   (  19-)  C  omega poor
2933 GLU   (  24-)  C  omega poor
2938 ALA   (  35-)  C  Poor phi/psi
2939 LYS   (  36-)  C  Poor phi/psi, omega poor
2941 ASP   (  38-)  C  omega poor
2950 LEU   (  47-)  C  Poor phi/psi
2955 ARG   (  52-)  C  Poor phi/psi
2956 ARG   (  53-)  C  Poor phi/psi
2957 SER   (  54-)  C  Poor phi/psi
2958 ASP   (  55-)  C  Poor phi/psi
2959 GLN   (  56-)  C  Poor phi/psi
2967 LEU   (  64-)  C  Poor phi/psi
2971 LEU   (  68-)  C  Poor phi/psi
2994 ALA   (  91-)  C  Poor phi/psi
2995 ASP   (  92-)  C  Poor phi/psi
3020 ALA   ( 125-)  C  Poor phi/psi
3021 ALA   ( 126-)  C  Poor phi/psi
3027 ALA   ( 132-)  C  Poor phi/psi
3033 ALA   ( 140-)  C  Poor phi/psi
3037 ALA   ( 144-)  C  Poor phi/psi
3041 ALA   ( 148-)  C  Poor phi/psi
3042 ALA   ( 149-)  C  Poor phi/psi
3046 ALA   ( 153-)  C  Poor phi/psi, omega poor
3053 ALA   ( 160-)  C  Poor phi/psi
3055 ALA   ( 162-)  C  Poor phi/psi
And so on for a total of 687 lines.

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

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

chi-1/chi-2 correlation Z-score : -5.590

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.

3327 SER   ( 212-)  D    0.33
4666 SER   ( 116-)  O    0.36
5338 ARG   (  28-)  U    0.36
6274 LYS   (  17-)  3    0.36
4801 SER   ( 133-)  P    0.38

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 OADE  (   7-)  A      0
   4 OURA  (   8-)  A      0
   5 OGUA  (   9-)  A      0
   6 OGUA  (  10-)  A      0
   7 OURA  (  11-)  A      0
   8 OADE  (  12-)  A      0
   9 OADE  (  13-)  A      0
  10 OGUA  (  14-)  A      0
  11 OGUA  (  15-)  A      0
  12 OGUA  (  16-)  A      0
  13 OCYT  (  17-)  A      0
  14 OCYT  (  18-)  A      0
  15 OCYT  (  19-)  A      0
  16 OADE  (  20-)  A      0
  17 OCYT  (  21-)  A      0
  18 OGUA  (  22-)  A      0
  19 OGUA  (  23-)  A      0
  20 OURA  (  24-)  A      0
  21 OGUA  (  25-)  A      0
  22 OGUA  (  26-)  A      0
  23 OADE  (  27-)  A      0
  24 OURA  (  28-)  A      0
  25 OGUA  (  29-)  A      0
  26 OCYT  (  30-)  A      0
  27 OCYT  (  31-)  A      0
And so on for a total of 4796 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 9.068

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!

3839 GLY   (  42-)  G   3.42   30
6395 GLY   (  50-)  5   2.90   13
6227 GLY   (  42-)  2   2.32   33
5383 GLY   (  73-)  U   2.25   21
3416 GLY   (  29-)  E   2.24   11
3215 GLY   ( 100-)  D   2.18   59
5755 GLY   (  22-)  Y   2.13   58
5243 GLY   (  69-)  T   2.06   10
6016 GLY   (   8-)  0   2.01   10
5147 GLY   (  81-)  S   1.82   80
2998 GLY   (  95-)  C   1.80   67
3338 GLY   ( 223-)  D   1.75   11
6326 GLY   (  45-)  4   1.74   80
6170 GLY   (  79-)  1   1.69   17
3950 GLY   ( 154-)  G   1.63   41
2993 GLY   (  90-)  C   1.60   76
6073 GLY   (  65-)  0   1.58   18
4737 GLY   (  69-)  P   1.54   16

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...

3878 LYS   (  81-)  G   1.58
5089 ARG   (  23-)  S   1.62
5203 ARG   (  29-)  T   3.73

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]

3347 PRO   ( 232-)  D    0.17 LOW
3657 PRO   (  66-)  F    0.46 HIGH
3938 PRO   ( 142-)  G    0.20 LOW
4169 PRO   (  32-)  I    0.15 LOW
5194 PRO   (  20-)  T    0.06 LOW
6135 PRO   (  44-)  1    0.11 LOW
6203 PRO   (  18-)  2    0.14 LOW
6352 PRO   (   7-)  5    0.05 LOW
6377 PRO   (  32-)  5    0.12 LOW
6456 PRO   (   7-)  7    0.13 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].

3123 PRO   (   8-)  D   -50.4 half-chair C-beta/C-alpha (-54 degrees)
3151 PRO   (  36-)  D   -40.3 envelop C-alpha (-36 degrees)
3239 PRO   ( 124-)  D  -127.1 half-chair C-delta/C-gamma (-126 degrees)
3334 PRO   ( 219-)  D  -113.5 envelop C-gamma (-108 degrees)
3356 PRO   ( 241-)  D    32.6 envelop C-delta (36 degrees)
3364 PRO   ( 249-)  D  -132.2 half-chair C-delta/C-gamma (-126 degrees)
3461 PRO   (  74-)  E   107.2 envelop C-beta (108 degrees)
3473 PRO   (  86-)  E   -32.1 envelop C-alpha (-36 degrees)
3513 PRO   ( 126-)  E  -128.4 half-chair C-delta/C-gamma (-126 degrees)
3525 PRO   ( 138-)  E   -47.9 half-chair C-beta/C-alpha (-54 degrees)
3564 PRO   ( 177-)  E  -115.7 envelop C-gamma (-108 degrees)
3576 PRO   ( 189-)  E  -129.4 half-chair C-delta/C-gamma (-126 degrees)
3616 PRO   (  25-)  F  -156.6 half-chair N/C-delta (-162 degrees)
3657 PRO   (  66-)  F   115.9 envelop C-beta (108 degrees)
3693 PRO   ( 102-)  F   103.5 envelop C-beta (108 degrees)
3769 PRO   ( 178-)  F  -113.3 envelop C-gamma (-108 degrees)
3799 PRO   (   2-)  G   113.7 envelop C-beta (108 degrees)
3884 PRO   (  87-)  G   154.9 half-chair C-alpha/N (162 degrees)
3909 PRO   ( 112-)  G   126.0 half-chair C-beta/C-alpha (126 degrees)
3979 PRO   (  12-)  H  -112.1 envelop C-gamma (-108 degrees)
4003 PRO   (  36-)  H   -62.4 half-chair C-beta/C-alpha (-54 degrees)
4093 PRO   ( 126-)  H  -113.1 envelop C-gamma (-108 degrees)
4095 PRO   ( 128-)  H   -31.5 envelop C-alpha (-36 degrees)
4121 PRO   ( 154-)  H   -27.4 envelop C-alpha (-36 degrees)
4135 PRO   ( 168-)  H   -64.3 envelop C-beta (-72 degrees)
And so on for a total of 66 lines.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

6412 GLU   (  15-)  6      CD  <-> 6440 CYS   (  43-)  6      SG     1.13    2.27  INTRA BF
6412 GLU   (  15-)  6      OE2 <-> 6440 CYS   (  43-)  6      SG     1.06    1.94  INTRA BF
6573 CYS   (  14-)  9      SG  <-> 6591 HIS   (  32-)  9      ND1    1.01    2.29  INTRA BL
6412 GLU   (  15-)  6      OE1 <-> 6440 CYS   (  43-)  6      SG     1.00    2.00  INTRA BF
6586 CYS   (  27-)  9      SG  <-> 6591 HIS   (  32-)  9      ND1    0.93    2.37  INTRA BL
4726 THR   (  58-)  P      O   <-> 4729 ARG   (  61-)  P      NE     0.91    1.79  INTRA BF
3492 THR   ( 105-)  E      OG1 <-> 3586 ARG   ( 199-)  E      NH2    0.84    1.86  INTRA BF
  88 OGUA  (  92-)  A      N3  <-> 6232 ASN   (  47-)  2      ND2    0.80    2.20  INTRA BL
1288 OGUA  (1377-)  A      N2  <-> 1556 OADE  (1654-)  A      O2'    0.76    1.94  INTRA BL
4726 THR   (  58-)  P      O   <-> 4729 ARG   (  61-)  P      CZ     0.74    2.06  INTRA BL
5813 LYS   (  81-)  Y      NZ  <-> 5831 CYS   (  99-)  Y      SG     0.74    2.56  INTRA BF
6570 CYS   (  11-)  9      SG  <-> 6586 CYS   (  27-)  9      SG     0.72    2.73  INTRA BL
1172 OCYT  (1261-)  A      OP2 <-> 5325 LYS   (  15-)  U      NZ     0.70    2.00  INTRA BL
  22 OGUA  (  26-)  A      N2  <->  526 OGUA  ( 536-)  A      O2'    0.68    2.02  INTRA BL
2559 OCYT  (2657-)  A      OP2 <-> 2646 OGUA  (2744-)  A      O2'    0.67    1.73  INTRA BF
1030 OGUA  (1067-)  A      N2  <-> 1098 OADE  (1187-)  A      C2     0.66    2.44  INTRA BL
1606 OCYT  (1704-)  A      OP1 <-> 3519 HIS   ( 132-)  E      ND1    0.65    2.05  INTRA BL
 549 OCYT  ( 559-)  A      O3' <-> 5363 ARG   (  53-)  U      NH1    0.64    2.06  INTRA BL
1257 OADE  (1346-)  A      O2' <-> 1258 OADE  (1347-)  A      C2'    0.62    2.18  INTRA BL
6570 CYS   (  11-)  9      SG  <-> 6573 CYS   (  14-)  9      SG     0.59    2.86  INTRA BL
2545 OADE  (2643-)  A      O2' <-> 3448 ARG   (  61-)  E      NH2    0.59    2.11  INTRA BF
1991 OURA  (2089-)  A      N3  <-> 2343 OADE  (2441-)  A      C2     0.58    2.52  INTRA BL
3128 ARG   (  13-)  D      NH1 <-> 3131 MET   (  16-)  D      SD     0.58    2.72  INTRA BF
4732 LYS   (  64-)  P      O   <-> 4734 GLY   (  66-)  P      N      0.58    2.12  INTRA BL
 950 OURA  ( 987-)  A      OP2 <-> 4706 GLN   (  38-)  P      CD     0.57    2.23  INTRA BL
And so on for a total of 3676 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: 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: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: 0

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: 9

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.

3359 ARG   ( 244-)  D      -8.70
4689 ARG   (  21-)  P      -8.63
3354 ARG   ( 239-)  D      -8.61
4599 ARG   (  49-)  O      -8.47
3665 ARG   (  74-)  F      -8.43
5269 ARG   (  95-)  T      -8.14
5943 ARG   ( 112-)  Z      -8.13
4823 ARG   (   5-)  Q      -8.12
4686 ARG   (  18-)  P      -7.93
4901 MET   (  83-)  Q      -7.93
6397 TYR   (  52-)  5      -7.91
5063 ARG   ( 105-)  R      -7.88
6400 ARG   (  55-)  5      -7.79
6172 ARG   (  81-)  1      -7.79
4900 ARG   (  82-)  Q      -7.78
4824 ARG   (   6-)  Q      -7.75
6441 ARG   (  44-)  6      -7.74
6496 ARG   (  47-)  7      -7.69
4735 MET   (  67-)  P      -7.66
4832 ARG   (  14-)  Q      -7.65
6022 ARG   (  14-)  0      -7.64
3378 ARG   ( 263-)  D      -7.61
3538 TYR   ( 151-)  E      -7.60
6028 ARG   (  20-)  0      -7.57
3357 ARG   ( 242-)  D      -7.57
And so on for a total of 343 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.

2927 LYS   (  18-)  C      2929 - TYR     20- ( C)         -5.09
2937 THR   (  34-)  C      2940 - PHE     37- ( C)         -4.65
3153 LYS   (  38-)  D      3156 - GLY     41- ( D)         -4.54
3173 HIS   (  58-)  D      3175 - ARG     60- ( D)         -5.19
3351 GLY   ( 236-)  D      3354 - ARG    239- ( D)         -5.75
3356 PRO   ( 241-)  D      3359 - ARG    244- ( D)         -6.22
3514 ASP   ( 127-)  E      3516 - HIS    129- ( E)         -4.92
3530 ASN   ( 143-)  E      3533 - THR    146- ( E)         -5.39
3635 ARG   (  44-)  F      3637 - ARG     46- ( F)         -5.84
3658 GLN   (  67-)  F      3660 - HIS     69- ( F)         -5.65
3673 ILE   (  82-)  F      3675 - VAL     84- ( F)         -5.29
4124 TYR   ( 157-)  H      4127 - LYS    160- ( H)         -5.24
4240 ARG   ( 103-)  I      4242 - HIS    105- ( I)         -5.43
4419 LYS   (   7-)  N      4422 - GLU     10- ( N)         -4.74
4597 ILE   (  47-)  O      4599 - ARG     49- ( O)         -5.65
4682 LYS   (  14-)  P      4686 - ARG     18- ( P)         -6.23
4703 HIS   (  35-)  P      4707 - LYS     39- ( P)         -5.50
4717 ARG   (  49-)  P      4721 - GLY     53- ( P)         -5.08
4732 LYS   (  64-)  P      4736 - GLN     68- ( P)         -5.77
4742 GLU   (  74-)  P      4745 - ARG     77- ( P)         -5.36
4823 ARG   (   5-)  Q      4836 - LYS     18- ( Q)         -6.18
4900 ARG   (  82-)  Q      4903 - LYS     85- ( Q)         -6.43
4961 HIS   (   3-)  R      4963 - LYS      5- ( R)         -6.11
4965 GLY   (   7-)  R      4970 - ARG     12- ( R)         -4.91
5060 GLU   ( 102-)  R      5063 - ARG    105- ( R)         -5.64
And so on for a total of 51 lines.

Error: Abnormal average packing environment

The average packing score for the structure is very low.

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

Average for range 1 - 6596 : -2.047

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: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: V

Note: Quality value plot

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

Chain identifier: W

Note: Quality value plot

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

Chain identifier: X

Note: Quality value plot

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

Chain identifier: Y

Note: Quality value plot

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

Chain identifier: Z

Note: Quality value plot

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

Chain identifier: 0

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: 1

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: 2

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: 3

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: 4

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: 5

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: 6

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: 7

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: 8

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: 9

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.

6020 ASN   (  12-)  0   -4.05
3659 LYS   (  68-)  F   -3.80
4457 ASN   (  45-)  N   -3.50
5079 ARG   (  13-)  S   -3.47
3760 ASN   ( 169-)  F   -3.40
6354 LYS   (   9-)  5   -3.36
5315 LYS   (   5-)  U   -3.29
3536 ARG   ( 149-)  E   -3.28
4965 GLY   (   7-)  R   -3.27
4707 LYS   (  39-)  P   -3.26
3686 ARG   (  95-)  F   -3.17
4962 LEU   (   4-)  R   -3.17
4836 LYS   (  18-)  Q   -3.16
4723 ARG   (  55-)  P   -3.13
4963 LYS   (   5-)  R   -3.12
4414 LYS   (   2-)  N   -3.11
4689 ARG   (  21-)  P   -3.11
3530 ASN   ( 143-)  E   -3.07
4686 ARG   (  18-)  P   -3.06
6527 HIS   (  31-)  8   -3.05
3658 GLN   (  67-)  F   -3.04
6456 PRO   (   7-)  7   -3.04
5735 ARG   (   2-)  Y   -3.03
5780 LYS   (  47-)  Y   -3.03
3534 PRO   ( 147-)  E   -3.01
And so on for a total of 116 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.

3121 PHE   (   6-)  D     - 3124 TYR   (   9-)  D        -1.79
3155 THR   (  40-)  D     - 3158 ARG   (  43-)  D        -1.85
3159 ASN   (  44-)  D     - 3163 ARG   (  48-)  D        -2.12
3342 ASN   ( 227-)  D     - 3345 ASP   ( 230-)  D        -2.12
3351 GLY   ( 236-)  D     - 3360 PRO   ( 245-)  D        -2.29
3446 VAL   (  59-)  E     - 3449 PRO   (  62-)  E        -2.15
3518 ALA   ( 131-)  E     - 3522 HIS   ( 135-)  E        -2.04
3524 HIS   ( 137-)  E     - 3527 SER   ( 140-)  E        -2.24
3528 ILE   ( 141-)  E     - 3536 ARG   ( 149-)  E        -2.72
3636 ARG   (  45-)  F     - 3640 ALA   (  49-)  F        -1.81
3647 GLU   (  56-)  F     - 3651 SER   (  60-)  F        -1.81
3838 GLN   (  41-)  G     - 3841 GLY   (  44-)  G        -1.90
4412 ALA   ( 133-)  J     - 4415 THR   (   3-)  N        -1.51
4576 LYS   (  26-)  O     - 4579 ASN   (  29-)  O        -1.96
4681 ASN   (  13-)  P     - 4686 ARG   (  18-)  P        -2.16
4694 GLY   (  26-)  P     - 4699 ALA   (  31-)  P        -1.93
4705 GLY   (  37-)  P     - 4709 ARG   (  41-)  P        -2.07
4712 GLY   (  44-)  P     - 4718 ARG   (  50-)  P        -1.98
4720 GLU   (  52-)  P     - 4723 ARG   (  55-)  P        -2.41
4726 THR   (  58-)  P     - 4730 LEU   (  62-)  P        -2.21
4736 GLN   (  68-)  P     - 4741 GLY   (  73-)  P        -2.28
4742 GLU   (  74-)  P     - 4745 ARG   (  77-)  P        -2.21
4770 ARG   ( 102-)  P     - 4773 LEU   ( 105-)  P        -1.73
4774 LEU   ( 106-)  P     - 4777 GLY   ( 109-)  P        -2.01
4828 ARG   (  10-)  Q     - 4836 LYS   (  18-)  Q        -2.26
4899 VAL   (  81-)  Q     - 4902 GLY   (  84-)  Q        -2.11
4960 ARG   (   2-)  R     - 4963 LYS   (   5-)  R        -2.64
4967 LYS   (   9-)  R     - 4970 ARG   (  12-)  R        -1.74
5062 ARG   ( 104-)  R     - 5065 ASP   ( 107-)  R        -1.62
5157 PRO   (  91-)  S     - 5165 LYS   (  99-)  S        -2.09
5268 ALA   (  94-)  T     - 5272 LYS   (  98-)  T        -2.27
5301 ALA   ( 127-)  T     - 5305 ALA   ( 131-)  T        -1.83
5311 LYS   ( 137-)  T     - 5317 GLY   (   7-)  U        -2.34
5504 LYS   (  76-)  V     - 5509 TYR   (  81-)  V        -2.25
5615 LEU   (  86-)  W     - 5618 ALA   (  89-)  W        -1.93
5736 VAL   (   3-)  Y     - 5742 LYS   (   9-)  Y        -2.08
5801 HIS   (  68-)  Y     - 5804 LYS   (  71-)  Y        -1.53
6024 SER   (  16-)  0     - 6028 ARG   (  20-)  0        -2.21
6103 PRO   (  12-)  1     - 6106 ALA   (  15-)  1        -1.72
6346 CYS   (  65-)  4     - 6356 THR   (  11-)  5        -2.46
6365 ARG   (  20-)  5     - 6368 HIS   (  23-)  5        -1.99
6449 VAL   (  52-)  6     - 6452 ARG   (   3-)  7        -1.84
6453 THR   (   4-)  7     - 6456 PRO   (   7-)  7        -2.24
6525 LYS   (  29-)  8     - 6529 ASN   (  33-)  8        -2.45

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: 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: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: 0

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: 8

Note: Second generation quality Z-score plot

Chain identifier: 9

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.

3301 HIS   ( 186-)  D
3442 ASN   (  55-)  E
3519 HIS   ( 132-)  E
3567 ASN   ( 180-)  E
3660 HIS   (  69-)  F
4106 GLN   ( 139-)  H
4242 HIS   ( 105-)  I
4276 GLN   ( 139-)  I
4457 ASN   (  45-)  N
4540 HIS   ( 128-)  N
4579 ASN   (  29-)  O
4632 ASN   (  82-)  O
4681 ASN   (  13-)  P
4971 HIS   (  13-)  R
4981 ASN   (  23-)  R
5324 HIS   (  14-)  U
5376 ASN   (  66-)  U
5439 GLN   (  11-)  V
5586 ASN   (  57-)  W
5590 ASN   (  61-)  W
5640 HIS   ( 111-)  W
5695 ASN   (  55-)  X
5776 ASN   (  43-)  Y
5824 ASN   (  92-)  Y
5896 GLN   (  65-)  Z
5906 ASN   (  75-)  Z
6020 ASN   (  12-)  0
6136 ASN   (  45-)  1
6276 GLN   (  19-)  3
6290 GLN   (  33-)  3
6309 HIS   (  52-)  3
6327 ASN   (  46-)  4
6527 HIS   (  31-)  8
6529 ASN   (  33-)  8
6593 GLN   (  34-)  9

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.

   2 OGUA  (   6-)  A      N1
   9 OADE  (  13-)  A      N6
  23 OADE  (  27-)  A      N6
  39 OGUA  (  43-)  A      N2
  64 OGUA  (  68-)  A      N2
  70 OCYT  (  74-)  A      O2'
 131 OGUA  ( 135-)  A      N2
 133 OGUA  ( 137-)  A      N1
 133 OGUA  ( 137-)  A      N2
 135 OADE  ( 139-)  A      N6
 153 OGUA  ( 159-)  A      N1
 182 OURA  ( 188-)  A      N3
 208 OGUA  ( 214-)  A      N1
 228 OCYT  ( 234-)  A      N4
 229 OGUA  ( 235-)  A      N1
 230 OGUA  ( 236-)  A      N2
 241 OGUA  ( 247-)  A      N2
 254 OADE  ( 260-)  A      N6
 276 OGUA  ( 282-)  A      N2
 288 OURA  ( 295-)  A      N3
 320 OGUA  ( 330-)  A      N2
 321 OGUA  ( 331-)  A      N2
 322 OGUA  ( 332-)  A      N1
 343 OADE  ( 353-)  A      O2'
 359 OADE  ( 369-)  A      N6
And so on for a total of 735 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.

2947 HIS   (  44-)  C      NE2
3198 GLU   (  83-)  D      OE1
3211 HIS   (  96-)  D      ND1
3214 ASP   (  99-)  D      OD1
3258 HIS   ( 143-)  D      NE2
3313 ASN   ( 198-)  D      OD1
3460 GLU   (  73-)  E      OE2
3760 ASN   ( 169-)  F      OD1
3837 ASN   (  40-)  G      OD1
3901 GLU   ( 104-)  G      OE1
4462 ASP   (  50-)  N      OD2
4630 ASP   (  80-)  O      OD1
4720 GLU   (  52-)  P      OE1
4875 HIS   (  57-)  Q      ND1
4898 GLU   (  80-)  Q      OE2
4923 GLU   ( 105-)  Q      OE1
5007 ASP   (  49-)  R      OD1
5134 GLN   (  68-)  S      OE1
5185 GLU   (  11-)  T      OE1
5185 GLU   (  11-)  T      OE2
5281 ASP   ( 107-)  T      OD1
5382 HIS   (  72-)  U      ND1
5401 ASP   (  91-)  U      OD2
5404 ASN   (  94-)  U      OD1
5492 HIS   (  64-)  V      ND1
5591 HIS   (  62-)  W      ND1
5631 HIS   ( 102-)  W      NE2
5739 HIS   (   6-)  Y      NE2
5744 ASP   (  11-)  Y      OD1
5790 GLN   (  57-)  Y      OE1
5795 GLU   (  62-)  Y      OE2
6296 ASP   (  39-)  3      OD1
6388 HIS   (  43-)  5      ND1
6412 GLU   (  15-)  6      OE1
6417 ASN   (  20-)  6      OD1
6423 ASN   (  26-)  6      OD1
6446 HIS   (  49-)  6      NE2
6529 ASN   (  33-)  8      OD1

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.

2958 ASP   (  55-)  C   H-bonding suggests Asn
2990 GLU   (  87-)  C   H-bonding suggests Gln
2991 GLU   (  88-)  C   H-bonding suggests Gln; but Alt-Rotamer
3145 GLU   (  30-)  D   H-bonding suggests Gln
3460 GLU   (  73-)  E   H-bonding suggests Gln
3470 ASP   (  83-)  E   H-bonding suggests Asn
3550 GLU   ( 163-)  E   H-bonding suggests Gln
3614 ASP   (  23-)  F   H-bonding suggests Asn
3729 GLU   ( 138-)  F   H-bonding suggests Gln; but Alt-Rotamer
4013 GLU   (  46-)  H   H-bonding suggests Gln
4020 GLU   (  53-)  H   H-bonding suggests Gln
4083 GLU   ( 116-)  H   H-bonding suggests Gln
4091 GLU   ( 124-)  H   H-bonding suggests Gln; but Alt-Rotamer
4233 ASP   (  96-)  I   H-bonding suggests Asn
4259 GLU   ( 122-)  I   H-bonding suggests Gln; but Alt-Rotamer
4262 GLU   ( 125-)  I   H-bonding suggests Gln
4272 GLU   ( 135-)  I   H-bonding suggests Gln
4429 ASP   (  17-)  N   H-bonding suggests Asn
4470 ASP   (  58-)  N   H-bonding suggests Asn; but Alt-Rotamer
4559 GLU   (   9-)  O   H-bonding suggests Gln
4630 ASP   (  80-)  O   H-bonding suggests Asn; but Alt-Rotamer
4923 GLU   ( 105-)  Q   H-bonding suggests Gln
4956 ASP   ( 138-)  Q   H-bonding suggests Asn
5060 GLU   ( 102-)  R   H-bonding suggests Gln
5107 ASP   (  41-)  S   H-bonding suggests Asn
5185 GLU   (  11-)  T   H-bonding suggests Gln
5281 ASP   ( 107-)  T   H-bonding suggests Asn
5302 GLU   ( 128-)  T   H-bonding suggests Gln
5401 ASP   (  91-)  U   H-bonding suggests Asn; but Alt-Rotamer
5407 ASP   (  97-)  U   H-bonding suggests Asn; but Alt-Rotamer
5421 GLU   ( 111-)  U   H-bonding suggests Gln; but Alt-Rotamer
5471 GLU   (  43-)  V   H-bonding suggests Gln
5592 ASP   (  63-)  W   H-bonding suggests Asn
5638 GLU   ( 109-)  W   H-bonding suggests Gln
5715 ASP   (  75-)  X   H-bonding suggests Asn; but Alt-Rotamer
5762 GLU   (  29-)  Y   H-bonding suggests Gln
5773 GLU   (  40-)  Y   H-bonding suggests Gln
5797 GLU   (  64-)  Y   H-bonding suggests Gln
5842 GLU   (  11-)  Z   H-bonding suggests Gln
5908 ASP   (  77-)  Z   H-bonding suggests Asn; but Alt-Rotamer
5971 ASP   ( 140-)  Z   H-bonding suggests Asn
5976 GLU   ( 145-)  Z   H-bonding suggests Gln
6180 GLU   (  89-)  1   H-bonding suggests Gln; but Alt-Rotamer
6197 GLU   (  12-)  2   H-bonding suggests Gln
6212 GLU   (  27-)  2   H-bonding suggests Gln
6393 GLU   (  48-)  5   H-bonding suggests Gln
6404 GLU   (  59-)  5   H-bonding suggests Gln
6409 GLU   (  12-)  6   H-bonding suggests Gln; but Alt-Rotamer
6421 GLU   (  24-)  6   H-bonding suggests Gln
6550 GLU   (  54-)  8   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 :  -3.867 (poor)
  2nd generation packing quality :  -4.241 (bad)
  Ramachandran plot appearance   :  -5.100 (bad)
  chi-1/chi-2 rotamer normality  :  -5.590 (bad)
  Backbone conformation          :  -0.685

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.542 (tight)
  Bond angles                    :   0.903
  Omega angle restraints         :   1.649 (loose)
  Side chain planarity           :   0.538 (tight)
  Improper dihedral distribution :   0.861
  B-factor distribution          :   0.793
  Inside/Outside distribution    :   1.038

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 :  -2.4
  2nd generation packing quality :  -1.8
  Ramachandran plot appearance   :  -2.0
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.542 (tight)
  Bond angles                    :   0.903
  Omega angle restraints         :   1.649 (loose)
  Side chain planarity           :   0.538 (tight)
  Improper dihedral distribution :   0.861
  B-factor distribution          :   0.793
  Inside/Outside distribution    :   1.038
==============

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.