WHAT IF Check report

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

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

Verification log for pdb3o5h.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 437.110  B   = 288.380  C    = 306.560
    Alpha=  90.000  Beta=  99.130  Gamma=  90.000

Dimensions of a reduced cell

    A    = 288.380  B   = 306.560  C    = 437.110
    Alpha=  80.870  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 306.560  B   = 288.380  C    = 437.110
    Alpha=  90.000  Beta=  99.130  Gamma=  90.000

Transformation to conventional cell

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

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: 1698256.1
Volume of the Unit Cell V= 38143880.0
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 11.230
Vm by authors and this calculated Vm do not agree very well

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

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

Warning: Missing atoms

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

3486 ILE   (   4-)  A      CG1
3486 ILE   (   4-)  A      CG2
3486 ILE   (   4-)  A      CD1
3487 THR   (   5-)  A      OG1
3487 THR   (   5-)  A      CG2
3488 SER   (   6-)  A      OG
3489 SER   (   7-)  A      OG
3490 GLN   (   8-)  A      CG
3490 GLN   (   8-)  A      CD
3490 GLN   (   8-)  A      OE1
3490 GLN   (   8-)  A      NE2
3491 VAL   (   9-)  A      CG1
3491 VAL   (   9-)  A      CG2
3492 ARG   (  10-)  A      CG
3492 ARG   (  10-)  A      CD
3492 ARG   (  10-)  A      NE
3492 ARG   (  10-)  A      CZ
3492 ARG   (  10-)  A      NH1
3492 ARG   (  10-)  A      NH2
3493 GLU   (  11-)  A      CG
3493 GLU   (  11-)  A      CD
3493 GLU   (  11-)  A      OE1
3493 GLU   (  11-)  A      OE2
3494 HIS   (  12-)  A      CG
3494 HIS   (  12-)  A      ND1
And so on for a total of 15261 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

   1 OURA  (   3-)  1    High
   2 OURA  (   4-)  1    High
   3 OGUA  (   5-)  1    High
   4 OADE  (   6-)  1    High
   5 OCYT  (   7-)  1    High
   6 OCYT  (   8-)  1    High
   7 OURA  (   9-)  1    High
   8 OCYT  (  10-)  1    High
   9 OADE  (  11-)  1    High
  10 OADE  (  12-)  1    High
  11 OADE  (  13-)  1    High
  12 OURA  (  14-)  1    High
  13 OCYT  (  15-)  1    High
  14 OADE  (  16-)  1    High
  15 OGUA  (  17-)  1    High
  16 OGUA  (  18-)  1    High
  17 OURA  (  19-)  1    High
  18 OADE  (  20-)  1    High
  20 OGUA  (  22-)  1    High
  22 OGUA  (  24-)  1    High
  23 OURA  (  25-)  1    High
  24 OADE  (  26-)  1    High
  25 OCYT  (  27-)  1    High
  31 OGUA  (  33-)  1    High
  38 OADE  (  40-)  1    High
And so on for a total of 4336 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) : 90.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Nomenclature related problems

Warning: Phosphate group convention problem

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

  12 OURA  (  14-)  1
  14 OADE  (  16-)  1
  69 OADE  (  71-)  1
  70 OCYT  (  72-)  1
 147 OURA  ( 149-)  1
 156 OGUA  ( 158-)  1
 210 OGUA  ( 212-)  1
 250 OURA  ( 252-)  1
 303 OURA  ( 305-)  1
 324 OURA  ( 326-)  1
 325 OADE  ( 327-)  1
 337 OCYT  ( 339-)  1
 349 OADE  ( 351-)  1
 397 OADE  ( 399-)  1
 400 OADE  ( 402-)  1
 418 OGUA  ( 420-)  1
 419 OGUA  ( 421-)  1
 421 OADE  ( 423-)  1
 437 OCYT  ( 439-)  1
 467 OADE  ( 519-)  1
 472 OURA  ( 524-)  1
 526 OADE  ( 578-)  1
 527 OGUA  ( 579-)  1
 545 OGUA  ( 597-)  1
 560 OURA  ( 612-)  1
And so on for a total of 135 lines.

Error: Chain names not unique

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

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

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.

  37 OADE  (  39-)  1      N9   C4    1.34   -6.1
  43 OADE  (  45-)  1      N9   C4    1.33   -7.8
  50 OADE  (  52-)  1      N9   C4    1.40    4.3
  50 OADE  (  52-)  1      C6   N1    1.32   -4.2
  53 OGUA  (  55-)  1      N9   C4    1.34   -4.7
  58 OADE  (  60-)  1      N9   C4    1.35   -4.8
  68 OADE  (  70-)  1      N9   C4    1.41    6.3
  86 OADE  (  88-)  1      N9   C4    1.34   -5.4
  92 OGUA  (  94-)  1      N9   C4    1.31   -8.0
  92 OGUA  (  94-)  1      N3   C4    1.31   -5.5
  93 OADE  (  95-)  1      N9   C4    1.34   -5.4
  97 OADE  (  99-)  1      N3   C4    1.31   -5.8
  99 OGUA  ( 101-)  1      N9   C4    1.34   -5.0
 100 OCYT  ( 102-)  1      C1'  N1    1.52    4.4
 108 OGUA  ( 110-)  1      C1'  N9    1.50    4.3
 147 OURA  ( 149-)  1      C1'  N1    1.51    4.5
 155 OADE  ( 157-)  1      N9   C4    1.40    4.9
 155 OADE  ( 157-)  1      N3   C4    1.37    4.1
 187 OGUA  ( 189-)  1      C5   C4    1.35   -4.3
 187 OGUA  ( 189-)  1      N1   C2    1.34   -4.7
 187 OGUA  ( 189-)  1      C6   N1    1.35   -6.1
 217 OADE  ( 219-)  1      N9   C4    1.35   -4.5
 242 OGUA  ( 244-)  1      C6   O6    1.20   -4.3
 270 OGUA  ( 272-)  1      C6   N1    1.36   -5.0
 287 OADE  ( 289-)  1      N9   C4    1.35   -4.2
And so on for a total of 688 lines.

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

 |  1.002710 -0.000076 -0.000022|
 | -0.000076  1.002953 -0.000019|
 | -0.000022 -0.000019  1.002265|
Proposed new scale matrix

 |  0.002282  0.000000  0.000367|
 |  0.000000  0.003458  0.000000|
 |  0.000000  0.000000  0.003297|
With corresponding cell

    A    = 438.248  B   = 289.202  C    = 307.254
    Alpha=  90.003  Beta=  99.144  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 437.110  B   = 288.380  C    = 306.560
    Alpha=  90.000  Beta=  99.130  Gamma=  90.000

Variance: 12998.831
(Under-)estimated Z-score: 84.027

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.

   3 OGUA  (   5-)  1      N9   C8   N7  113.49    4.8
   7 OURA  (   9-)  1      C1'  N1   C2  122.87    4.3
   7 OURA  (   9-)  1      N1   C2   O2  126.47    5.2
   7 OURA  (   9-)  1      N3   C2   O2  118.90   -4.7
  15 OGUA  (  17-)  1      N9   C4   N3  128.96    4.9
  15 OGUA  (  17-)  1      C5   C4   N3  126.23   -4.7
  16 OGUA  (  18-)  1      N9   C8   N7  113.21    4.2
  18 OADE  (  20-)  1      C3'  C2'  C1' 105.18    4.1
  19 OGUA  (  21-)  1      N9   C8   N7  113.51    4.8
  20 OGUA  (  22-)  1      N9   C8   N7  114.01    5.8
  24 OADE  (  26-)  1      C8   N9   C4  103.93   -4.7
  24 OADE  (  26-)  1      C6   C5   C4  119.58    5.2
  24 OADE  (  26-)  1      N1   C2   N3  131.38    4.2
  26 OCYT  (  28-)  1      C1'  N1   C6  115.69   -4.3
  27 OCYT  (  29-)  1      N1   C2   O2  113.36   -9.2
  27 OCYT  (  29-)  1      N3   C2   O2  127.15    7.5
  30 OURA  (  32-)  1      C1'  N1   C6  134.04    9.2
  30 OURA  (  32-)  1      C1'  N1   C2  101.16  -13.8
  30 OURA  (  32-)  1      N1   C6   C5  117.95   -9.5
  30 OURA  (  32-)  1      N1   C2   O2  119.19   -5.2
  30 OURA  (  32-)  1      C6   N1   C2  124.64    6.1
  30 OURA  (  32-)  1      C5   C4   N3  117.19    4.3
  30 OURA  (  32-)  1      C4   N3   C2  122.24   -7.9
  30 OURA  (  32-)  1      O4   C4   N3  114.75   -6.6
  31 OGUA  (  33-)  1      N9   C8   N7  113.58    5.0
And so on for a total of 5954 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.

5816 PRO   (   8-)  K      CA    -6.3    29.21    38.15
6672 PRO   ( 121-)  P      CA    -6.3    29.20    38.15
7031 PRO   ( 143-)  R      CA    -6.9    28.45    38.15
The average deviation= 0.817

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.

6800 LEU   (  52-)  Q    8.27
4122 GLU   ( 190-)  C    8.24
7641 ALA   (  18-)  X    8.01
4199 ALA   ( 267-)  C    7.94
4793 GLU   ( 237-)  E    7.87
6609 LEU   (  58-)  P    7.81
8021 VAL   (  33-)  A    7.40
4128 ARG   ( 196-)  C    6.74
8199 LYS   ( 123-)  B    6.62
6658 GLY   ( 107-)  P    6.60
6627 PRO   (  76-)  P    6.49
6346 GLU   ( 107-)  N    6.37
5590 PHE   ( 175-)  I    6.14
6181 PHE   (  66-)  M    5.97
3937 LYS   (   5-)  C    5.89
5008 GLN   ( 157-)  F    5.85
4754 TYR   ( 198-)  E    5.75
4925 VAL   (  74-)  F    5.71
4900 GLY   (  49-)  F    5.71
5195 GLN   ( 197-)  G    5.66
6673 GLN   ( 122-)  P    5.65
5572 ASN   ( 157-)  I    5.64
6708 GLU   ( 157-)  P    5.64
6253 LEU   (  14-)  N    5.62
7340 GLU   ( 107-)  T    5.55
And so on for a total of 140 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.710

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 : -8.379

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.

7773 GLY   (  30-)  Y    -2.5
8318 GLY   (  50-)  D    -2.4
7779 GLY   (  36-)  Y    -2.4
3809 GLY   ( 121-)  B    -2.4
5175 GLY   ( 177-)  G    -2.4
6113 GLY   ( 140-)  L    -2.4
6646 GLY   (  95-)  P    -2.4
3944 GLY   (  12-)  C    -2.4
6162 GLY   (  47-)  M    -2.4
8528 GLY   (  53-)  G    -2.4
6854 GLY   ( 106-)  Q    -2.4
3711 GLY   (  13-)  B    -2.4
7715 GLY   (  92-)  X    -2.3
3900 GLY   ( 212-)  B    -2.3
3819 GLY   ( 131-)  B    -2.3
3779 GLY   (  91-)  B    -2.3
4483 GLY   ( 192-)  D    -2.3
7885 GLY   ( 142-)  Y    -2.3
5943 GLY   ( 135-)  K    -2.2
8440 GLY   (  52-)  F    -2.2
4582 GLY   (  26-)  E    -2.2
5347 GLY   ( 182-)  H    -2.2
4670 GLY   ( 114-)  E    -2.2
8525 GLY   (  50-)  G    -2.2
6538 GLY   ( 173-)  O    -2.2
And so on for a total of 70 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.

3488 SER   (   6-)  A  Poor phi/psi
3496 LYS   (  14-)  A  Poor phi/psi
3497 GLU   (  15-)  A  Poor phi/psi
3499 LEU   (  17-)  A  Poor phi/psi
3500 LYS   (  18-)  A  Poor phi/psi
3504 GLU   (  22-)  A  Poor phi/psi
3506 LYS   (  24-)  A  Poor phi/psi
3507 LYS   (  25-)  A  Poor phi/psi
3510 PHE   (  28-)  A  Poor phi/psi
3513 THR   (  31-)  A  Poor phi/psi
3518 VAL   (  36-)  A  Poor phi/psi
3520 LEU   (  38-)  A  Poor phi/psi
3523 TYR   (  41-)  A  Poor phi/psi
3525 PRO   (  43-)  A  Poor phi/psi
3526 GLN   (  44-)  A  Poor phi/psi
3529 LYS   (  47-)  A  Poor phi/psi
3531 PHE   (  49-)  A  Poor phi/psi
3535 LEU   (  53-)  A  omega poor
3536 LYS   (  54-)  A  omega poor
3537 LEU   (  55-)  A  Poor phi/psi
3538 PRO   (  56-)  A  Poor phi/psi
3539 ASN   (  57-)  A  Poor phi/psi
3542 ARG   (  60-)  A  Poor phi/psi
3544 ASN   (  62-)  A  Poor phi/psi
3552 ASP   (  70-)  A  Poor phi/psi
And so on for a total of 2167 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

4416 SER   ( 124-)  D    0.35
4608 VAL   (  52-)  E    0.36
5148 SER   ( 142-)  G    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 OGUA  (   5-)  1      0
   4 OADE  (   6-)  1      0
   5 OCYT  (   7-)  1      0
   6 OCYT  (   8-)  1      0
   7 OURA  (   9-)  1      0
   8 OCYT  (  10-)  1      0
   9 OADE  (  11-)  1      0
  10 OADE  (  12-)  1      0
  11 OADE  (  13-)  1      0
  12 OURA  (  14-)  1      0
  13 OCYT  (  15-)  1      0
  14 OADE  (  16-)  1      0
  15 OGUA  (  17-)  1      0
  16 OGUA  (  18-)  1      0
  17 OURA  (  19-)  1      0
  18 OADE  (  20-)  1      0
  19 OGUA  (  21-)  1      0
  20 OGUA  (  22-)  1      0
  21 OADE  (  23-)  1      0
  22 OGUA  (  24-)  1      0
  23 OURA  (  25-)  1      0
  24 OADE  (  26-)  1      0
  25 OCYT  (  27-)  1      0
  26 OCYT  (  28-)  1      0
  27 OCYT  (  29-)  1      0
And so on for a total of 6938 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -2.763

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 : 8.715

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!

3852 GLY   ( 164-)  B   3.36   15
3652 GLY   ( 170-)  A   3.35   12
3900 GLY   ( 212-)  B   3.23   14
6075 GLY   ( 102-)  L   3.04   42
4023 GLY   (  91-)  C   2.80   12
7859 GLY   ( 116-)  Y   2.76   15
6562 GLY   (  11-)  P   2.61   21
4712 GLY   ( 156-)  E   2.53   17
4431 GLY   ( 139-)  D   2.42   14
4030 GLY   (  98-)  C   2.33   10
3779 GLY   (  91-)  B   2.22   10
4705 GLY   ( 149-)  E   2.16   19
5563 GLY   ( 148-)  I   2.15   30
4247 GLY   ( 315-)  C   2.02   23
5781 GLY   ( 188-)  J   2.00   29
7800 GLY   (  57-)  Y   1.87   25
7389 GLY   (  43-)  U   1.84   20
7457 GLY   ( 111-)  U   1.81   18
5285 LYS   ( 120-)  H   1.73   14
3798 GLY   ( 110-)  B   1.71   25
7200 ALA   ( 154-)  S   1.68   20
8501 VAL   (  26-)  G   1.67   80
7174 LYS   ( 128-)  S   1.66   15
8494 GLY   (  19-)  G   1.62   29
6697 GLY   ( 146-)  P   1.60   37
5717 GLY   ( 124-)  J   1.56   27
8542 GLY   (  67-)  G   1.56   26
6570 LEU   (  19-)  P   1.54   23
4166 GLY   ( 234-)  C   1.52   14
7663 ARG   (  40-)  X   1.52   21
6144 GLY   (  29-)  M   1.51   51
7853 GLY   ( 110-)  Y   1.51   14
6596 GLY   (  45-)  P   1.50   25

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...

4136 ALA   ( 204-)  C   1.87
4555 THR   ( 266-)  D   1.96
4597 LYS   (  41-)  E   1.64
4865 ASP   (  14-)  F   2.30
4901 LYS   (  50-)  F   2.46
5935 PHE   ( 127-)  K   1.67
6262 ILE   (  23-)  N   1.93
6403 ARG   (  38-)  O   1.88
6666 LYS   ( 115-)  P   1.52
7100 ALA   (  54-)  S   1.87
7787 ASN   (  44-)  Y   1.98
7830 ARG   (  87-)  Y   1.65
8014 LYS   (  26-)  A   1.73

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]

3525 PRO   (  43-)  A    0.00 LOW
3538 PRO   (  56-)  A    0.00 LOW
3541 PRO   (  59-)  A    0.00 LOW
3543 PRO   (  61-)  A    0.00 LOW
3603 PRO   ( 121-)  A    0.00 LOW
3608 PRO   ( 126-)  A    0.00 LOW
3617 PRO   ( 135-)  A    0.00 LOW
3619 PRO   ( 137-)  A    0.00 LOW
3694 PRO   ( 212-)  A    0.00 LOW
3751 PRO   (  57-)  B    0.00 LOW
3760 PRO   (  66-)  B    0.00 LOW
3791 PRO   ( 103-)  B    0.00 LOW
3796 PRO   ( 108-)  B    0.00 LOW
3808 PRO   ( 120-)  B    0.00 LOW
3829 PRO   ( 141-)  B    0.00 LOW
3839 PRO   ( 151-)  B    0.00 LOW
3866 PRO   ( 178-)  B    0.00 LOW
3885 PRO   ( 197-)  B    0.00 LOW
3894 PRO   ( 206-)  B    0.00 LOW
3898 PRO   ( 210-)  B    0.00 LOW
3941 PRO   (   9-)  C    0.00 LOW
3950 PRO   (  18-)  C    0.00 LOW
3965 PRO   (  33-)  C    0.00 LOW
3972 PRO   (  40-)  C    0.00 LOW
3995 PRO   (  63-)  C    0.00 LOW
And so on for a total of 186 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.

 451 OCYT  ( 503-)  1      O2  <->  536 OGUA  ( 588-)  1      N2     1.33    1.37  INTRA BL
 459 OGUA  ( 511-)  1      N2  <->  528 OCYT  ( 580-)  1      N3     1.25    1.75  INTRA BL
 461 OGUA  ( 513-)  1      N2  <->  525 OCYT  ( 577-)  1      N3     1.17    1.83  INTRA BL
2483 OADE  (2673-)  1      N6  <-> 2491 OURA  (2681-)  1      O4     1.08    1.62  INTRA BF
 479 OGUA  ( 531-)  1      N2  <->  509 OCYT  ( 561-)  1      O2     1.03    1.67  INTRA BL
 116 OURA  ( 118-)  1      O4  <->  148 OADE  ( 150-)  1      N6     0.98    1.72  INTRA BF
 451 OCYT  ( 503-)  1      C2  <->  536 OGUA  ( 588-)  1      N2     0.94    2.16  INTRA BL
1144 OCYT  (1196-)  1      C5  <-> 1145 OADE  (1197-)  1      N7     0.93    2.17  INTRA BL
2172 OCYT  (2362-)  1      N4  <-> 2186 OGUA  (2376-)  1      O6     0.88    1.82  INTRA BL
 459 OGUA  ( 511-)  1      N2  <->  527 OGUA  ( 579-)  1      C2     0.87    2.23  INTRA BL
 485 OADE  ( 537-)  1      N6  <->  504 OURA  ( 556-)  1      N3     0.86    1.99  INTRA BF
 539 OGUA  ( 591-)  1      N2  <->  540 OADE  ( 592-)  1      C1'    0.85    2.25  INTRA BF
 709 OADE  ( 761-)  1      N1  <->  718 OGUA  ( 770-)  1      N2     0.85    2.15  INTRA BF
2060 OGUA  (2250-)  1      N2  <-> 2077 OCYT  (2267-)  1      O2     0.84    1.86  INTRA BF
 459 OGUA  ( 511-)  1      N2  <->  528 OCYT  ( 580-)  1      C4     0.83    2.27  INTRA BL
 554 OCYT  ( 606-)  1      C3' <->  555 OADE  ( 607-)  1      C8     0.83    2.27  INTRA BL
2483 OADE  (2673-)  1      N6  <-> 2491 OURA  (2681-)  1      C4     0.82    2.28  INTRA BF
2477 OADE  (2667-)  1      N6  <-> 2500 OGUA  (2690-)  1      N1     0.82    2.03  INTRA BL
 674 OGUA  ( 726-)  1      C6  <->  675 OGUA  ( 727-)  1      N1     0.81    2.29  INTRA BL
2499 OADE  (2689-)  1      N3  <-> 2512 OADE  (2702-)  1      C2     0.80    2.30  INTRA BL
 556 OADE  ( 608-)  1      N6  <->  557 OGUA  ( 609-)  1      N7     0.79    2.21  INTRA BL
1141 OADE  (1193-)  1      N7  <-> 1142 OGUA  (1194-)  1      N1     0.79    2.21  INTRA BL
  41 OADE  (  43-)  1      N7  <-> 2613 OADE  (2803-)  1      N6     0.78    2.22  INTRA BF
 116 OURA  ( 118-)  1      C4  <->  148 OADE  ( 150-)  1      N6     0.78    2.32  INTRA BF
 464 OADE  ( 516-)  1      N1  <->  522 OURA  ( 574-)  1      N3     0.77    2.23  INTRA BL
And so on for a total of 10000 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.247

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

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: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: V

Note: Quality value plot

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

Chain identifier: W

Note: Quality value plot

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

Chain identifier: X

Note: Quality value plot

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

Chain identifier: Y

Note: Quality value plot

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

Chain identifier: Z

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

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

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.

4510 ASN   ( 221-)  D   -4.29
3708 LYS   (  10-)  B   -4.21
6681 LYS   ( 130-)  P   -4.18
4064 LYS   ( 132-)  C   -4.18
7429 LYS   (  83-)  U   -4.17
6422 GLN   (  57-)  O   -4.16
8451 LYS   (  63-)  F   -4.16
7333 LYS   ( 100-)  T   -4.15
3588 LYS   ( 106-)  A   -4.15
8443 LYS   (  55-)  F   -4.08
8344 LYS   (   5-)  E   -4.08
3952 LYS   (  20-)  C   -4.07
3937 LYS   (   5-)  C   -4.07
7753 LYS   (  10-)  Y   -4.06
5585 LYS   ( 170-)  I   -4.03
3705 ASN   (   7-)  B   -4.03
5207 ASN   ( 209-)  G   -4.02
8488 LYS   (  13-)  G   -4.02
7128 LYS   (  82-)  S   -4.01
6477 ASN   ( 112-)  O   -4.00
7770 LYS   (  27-)  Y   -4.00
3893 ASN   ( 205-)  B   -4.00
3781 LYS   (  93-)  B   -3.99
6820 GLN   (  72-)  Q   -3.98
3876 LYS   ( 188-)  B   -3.98
And so on for a total of 1432 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.

3489 SER   (   7-)  A     - 3501 TYR   (  19-)  A        -2.10
3505 THR   (  23-)  A     - 3508 ARG   (  26-)  A        -2.49
3509 ASN   (  27-)  A     - 3512 GLU   (  30-)  A        -2.24
3513 THR   (  31-)  A     - 3518 VAL   (  36-)  A        -2.60
3519 GLY   (  37-)  A     - 3523 TYR   (  41-)  A        -2.08
3524 ASP   (  42-)  A     - 3531 PHE   (  49-)  A        -2.47
3534 SER   (  52-)  A     - 3537 LEU   (  55-)  A        -2.45
3540 CYS   (  58-)  A     - 3545 MET   (  63-)  A        -2.88
3546 SER   (  64-)  A     - 3550 PHE   (  68-)  A        -2.22
3561 SER   (  79-)  A     - 3565 ASP   (  83-)  A        -2.42
3571 ASP   (  89-)  A     - 3585 LEU   ( 103-)  A        -2.44
3586 SER   ( 104-)  A     - 3590 ASN   ( 108-)  A        -2.96
3594 ALA   ( 112-)  A     - 3600 LYS   ( 118-)  A        -2.28
3603 PRO   ( 121-)  A     - 3606 LEU   ( 124-)  A        -2.39
3614 GLY   ( 132-)  A     - 3617 PRO   ( 135-)  A        -2.27
3635 SER   ( 153-)  A     - 3643 LYS   ( 161-)  A        -2.68
3644 VAL   ( 162-)  A     - 3647 LEU   ( 165-)  A        -2.45
3652 GLY   ( 170-)  A     - 3657 GLU   ( 175-)  A        -1.87
3658 GLU   ( 176-)  A     - 3662 VAL   ( 180-)  A        -2.27
3663 ASN   ( 181-)  A     - 3668 SER   ( 186-)  A        -2.47
3669 VAL   ( 187-)  A     - 3673 VAL   ( 191-)  A        -2.24
3674 SER   ( 192-)  A     - 3678 LYS   ( 196-)  A        -2.18
3685 SER   ( 203-)  A     - 3689 LYS   ( 207-)  A        -2.26
3695 ALA   ( 213-)  A     - 3698 LEU   ( 216-)  A        -2.37
3700 GLY   (   2-)  B     - 3714 PHE   (  16-)  B        -2.66
And so on for a total of 415 lines.

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Water, ion, and hydrogenbond related checks

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   1 OURA  (   3-)  1      N3
  16 OGUA  (  18-)  1      N1
  20 OGUA  (  22-)  1      N1
  20 OGUA  (  22-)  1      N2
  23 OURA  (  25-)  1      N3
  38 OADE  (  40-)  1      N6
  42 OURA  (  44-)  1      N3
  44 OURA  (  46-)  1      N3
  46 OADE  (  48-)  1      N6
  57 OGUA  (  59-)  1      N1
  62 OGUA  (  64-)  1      N1
  63 OADE  (  65-)  1      N6
  67 OCYT  (  69-)  1      N4
  83 OADE  (  85-)  1      N6
  84 OGUA  (  86-)  1      N2
  85 OURA  (  87-)  1      N3
  97 OADE  (  99-)  1      N6
 118 OGUA  ( 120-)  1      N1
 124 OURA  ( 126-)  1      N3
 143 OGUA  ( 145-)  1      N1
 180 OURA  ( 182-)  1      N3
 195 OGUA  ( 197-)  1      N2
 208 OURA  ( 210-)  1      N3
 217 OADE  ( 219-)  1      N6
 232 OGUA  ( 234-)  1      N1
And so on for a total of 822 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:

  2nd generation packing quality : -11.976 (bad)
  Ramachandran plot appearance   :  -8.379 (bad)
  Backbone conformation          :  -2.763

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.063
  Bond angles                    :   1.553
  Omega angle restraints         :   1.585 (loose)
  Side chain planarity           :   0.000 (tight)
  Improper dihedral distribution :   0.806
  B-factor distribution          :   0.642
  Inside/Outside distribution    :   1.247 (unusual)

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 : 4.00


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -8.1 (bad)
  Ramachandran plot appearance   :  -4.9 (bad)
  Backbone conformation          :  -1.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.063
  Bond angles                    :   1.553
  Omega angle restraints         :   1.585 (loose)
  Side chain planarity           :   0.000 (tight)
  Improper dihedral distribution :   0.806
  B-factor distribution          :   0.642
  Inside/Outside distribution    :   1.247 (unusual)
==============

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.