WHAT IF Check report

This file was created 2012-01-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1u5s.ent

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

  71 HIS   (  71-)  A  1
 208 HIS   (  71-)  A  2
 345 HIS   (  71-)  A  3
 482 HIS   (  71-)  A  4
 619 HIS   (  71-)  A  5
 756 HIS   (  71-)  A  6
 893 HIS   (  71-)  A  7
1030 HIS   (  71-)  A  8
1167 HIS   (  71-)  A  9
1304 HIS   (  71-)  A 10
1441 HIS   (  71-)  A 11
1578 HIS   (  71-)  A 12
1715 HIS   (  71-)  A 13
1852 HIS   (  71-)  A 14
1989 HIS   (  71-)  A 15
2126 HIS   (  71-)  A 16
2263 HIS   (  71-)  A 17
2400 HIS   (  71-)  A 18

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; Model number 1

Note: Ramachandran plot

Chain identifier: B; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: B; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: B; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: B; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: B; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: B; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: B; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: B; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: B; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: B; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: B; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: B; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: B; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: B; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: B; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: B; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: B; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: B; Model number 18

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'.

  71 HIS   (  71-)  A      O
 208 HIS   (  71-)  A      O
 345 HIS   (  71-)  A      O
 482 HIS   (  71-)  A      O
 619 HIS   (  71-)  A      O
 756 HIS   (  71-)  A      O
 893 HIS   (  71-)  A      O
1030 HIS   (  71-)  A      O
1167 HIS   (  71-)  A      O
1304 HIS   (  71-)  A 1    O
1441 HIS   (  71-)  A 1    O
1578 HIS   (  71-)  A 1    O
1715 HIS   (  71-)  A 1    O
1852 HIS   (  71-)  A 1    O
1989 HIS   (  71-)  A 1    O
2126 HIS   (  71-)  A 1    O
2263 HIS   (  71-)  A 1    O
2400 HIS   (  71-)  A 1    O

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 GLN   (   1-)  A    Zero
   2 GLY   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 ARG   (   4-)  A    Zero
   5 VAL   (   5-)  A    Zero
   6 LEU   (   6-)  A    Zero
   7 HIS   (   7-)  A    Zero
   8 VAL   (   8-)  A    Zero
   9 VAL   (   9-)  A    Zero
  10 GLN   (  10-)  A    Zero
  11 THR   (  11-)  A    Zero
  14 PRO   (  14-)  A    Zero
  15 PHE   (  15-)  A    Zero
  16 SER   (  16-)  A    Zero
  17 SER   (  17-)  A    Zero
  18 VAL   (  18-)  A    Zero
  21 GLU   (  21-)  A    Zero
  22 GLU   (  22-)  A    Zero
  24 ASN   (  24-)  A    Zero
  26 GLU   (  26-)  A    Zero
  30 THR   (  30-)  A    Zero
  31 MET   (  31-)  A    Zero
  32 GLU   (  32-)  A    Zero
  33 VAL   (  33-)  A    Zero
  34 ILE   (  34-)  A    Zero
And so on for a total of 2160 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 112 PHE   ( 112-)  B      CA   CB    2.14   30.7
 112 PHE   ( 112-)  B      CB   CG    2.12   26.9
 137 VAL   ( 137-)  B      C    O     0.48  -37.8
 249 PHE   ( 112-)  B      CA   CB    2.15   30.8
 249 PHE   ( 112-)  B      CB   CG    2.12   26.9
 274 VAL   ( 137-)  B      C    O     0.47  -37.9
 386 PHE   ( 112-)  B      CA   CB    2.14   30.7
 386 PHE   ( 112-)  B      CB   CG    2.12   26.9
 411 VAL   ( 137-)  B      C    O     0.48  -37.8
 523 PHE   ( 112-)  B      CA   CB    2.14   30.7
 523 PHE   ( 112-)  B      CB   CG    2.12   26.9
 548 VAL   ( 137-)  B      C    O     0.47  -37.9
 660 PHE   ( 112-)  B      CA   CB    2.15   30.8
 660 PHE   ( 112-)  B      CB   CG    2.12   26.9
 685 VAL   ( 137-)  B      C    O     0.47  -37.8
 797 PHE   ( 112-)  B      CA   CB    2.14   30.6
 797 PHE   ( 112-)  B      CB   CG    2.12   26.9
 822 VAL   ( 137-)  B      C    O     0.47  -37.8
 934 PHE   ( 112-)  B      CA   CB    2.14   30.7
 934 PHE   ( 112-)  B      CB   CG    2.12   26.9
 959 VAL   ( 137-)  B      C    O     0.47  -37.8
1071 PHE   ( 112-)  B      CA   CB    2.14   30.7
1071 PHE   ( 112-)  B      CB   CG    2.12   26.9
1096 VAL   ( 137-)  B      C    O     0.47  -37.8
1208 PHE   ( 112-)  B      CA   CB    2.14   30.7
And so on for a total of 54 lines.

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 1.020
Model 2 : 1.017
Model 3 : 1.015
Model 4 : 1.017
Model 5 : 1.019
Model 6 : 1.019
Model 7 : 1.017
Model 8 : 1.019
Model 9 : 1.019
Model 10 : 1.020
Model 11 : 1.016
Model 12 : 1.017
Model 13 : 1.018
Model 14 : 1.016
Model 15 : 1.018
Model 16 : 1.017
Model 17 : 1.018
Model 18 : 1.018

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

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.

   7 HIS   (   7-)  A      CA   CB   CG  109.45   -4.3
  71 HIS   (  71-)  A      CA   CB   CG  109.58   -4.2
 102 HIS   ( 102-)  B      CA   CB   CG  109.27   -4.5
 103 PHE   ( 103-)  B      CA   CB   CG  108.51   -5.3
 112 PHE   ( 112-)  B      N    CA   CB  134.93   14.4
 112 PHE   ( 112-)  B      CA   CB   CG   71.08  -42.7
 112 PHE   ( 112-)  B      CB   CG   CD1 145.60   14.6
 112 PHE   ( 112-)  B      CB   CG   CD2  92.75  -16.4
 115 HIS   ( 115-)  B      CA   CB   CG  109.76   -4.0
 117 HIS   ( 117-)  B      CA   CB   CG  109.33   -4.5
 129 HIS   ( 129-)  B      CA   CB   CG  108.40   -5.4
 134 PHE   ( 134-)  B      CA   CB   CG  109.63   -4.2
 137 VAL   ( 137-)  B      CA   C    O    70.94  -29.3
 144 HIS   (   7-)  A      CA   CB   CG  109.42   -4.4
 208 HIS   (  71-)  A      CA   CB   CG  109.54   -4.3
 239 HIS   ( 102-)  B      CA   CB   CG  109.34   -4.5
 240 PHE   ( 103-)  B      CA   CB   CG  108.41   -5.4
 249 PHE   ( 112-)  B      N    CA   CB  134.88   14.3
 249 PHE   ( 112-)  B      CA   CB   CG   71.13  -42.7
 249 PHE   ( 112-)  B      CB   CG   CD1 145.56   14.6
 249 PHE   ( 112-)  B      CB   CG   CD2  92.69  -16.5
 252 HIS   ( 115-)  B      CA   CB   CG  109.70   -4.1
 254 HIS   ( 117-)  B      CA   CB   CG  109.38   -4.4
 266 HIS   ( 129-)  B      CA   CB   CG  108.29   -5.5
 271 PHE   ( 134-)  B      CA   CB   CG  109.56   -4.2
And so on for a total of 234 lines.

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 1.071
Model 2 : 1.073
Model 3 : 1.073
Model 4 : 1.072
Model 5 : 1.072
Model 6 : 1.072
Model 7 : 1.072
Model 8 : 1.071
Model 9 : 1.072
Model 10 : 1.073
Model 11 : 1.072
Model 12 : 1.072
Model 13 : 1.072
Model 14 : 1.073
Model 15 : 1.073
Model 16 : 1.073
Model 17 : 1.073
Model 18 : 1.072

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.

 112 PHE   ( 112-)  B      CA    -8.0    21.22    33.98
 249 PHE   ( 112-)  B      CA    -7.9    21.27    33.98
 386 PHE   ( 112-)  B      CA    -8.0    21.15    33.98
 523 PHE   ( 112-)  B      CA    -8.0    21.16    33.98
 660 PHE   ( 112-)  B      CA    -8.0    21.20    33.98
 797 PHE   ( 112-)  B      CA    -8.0    21.25    33.98
 934 PHE   ( 112-)  B      CA    -8.0    21.17    33.98
1071 PHE   ( 112-)  B      CA    -8.0    21.21    33.98
1208 PHE   ( 112-)  B      CA    -8.0    21.17    33.98
1345 PHE   ( 112-)  B 1    CA    -8.0    21.20    33.98
1482 PHE   ( 112-)  B 1    CA    -8.0    21.22    33.98
1619 PHE   ( 112-)  B 1    CA    -7.9    21.30    33.98
1756 PHE   ( 112-)  B 1    CA    -8.0    21.17    33.98
1893 PHE   ( 112-)  B 1    CA    -8.0    21.20    33.98
2030 PHE   ( 112-)  B 1    CA    -8.0    21.25    33.98
2167 PHE   ( 112-)  B 1    CA    -8.0    21.15    33.98
2304 PHE   ( 112-)  B 1    CA    -8.0    21.19    33.98
2441 PHE   ( 112-)  B 1    CA    -8.0    21.15    33.98
The average deviation= 1.098

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 1.072
Model 2 : 1.071
Model 3 : 1.069
Model 4 : 1.069
Model 5 : 1.071
Model 6 : 1.068
Model 7 : 1.069
Model 8 : 1.067
Model 9 : 1.067
Model 10 : 1.071
Model 11 : 1.068
Model 12 : 1.066
Model 13 : 1.074
Model 14 : 1.073
Model 15 : 1.069
Model 16 : 1.072
Model 17 : 1.069
Model 18 : 1.072

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 112 PHE   ( 112-)  B      CB   6.13
1208 PHE   ( 112-)  B      CB   6.12
1756 PHE   ( 112-)  B 1    CB   6.12
1893 PHE   ( 112-)  B 1    CB   6.11
 660 PHE   ( 112-)  B      CB   6.11
2441 PHE   ( 112-)  B 1    CB   6.11
 934 PHE   ( 112-)  B      CB   6.10
1345 PHE   ( 112-)  B 1    CB   6.10
2304 PHE   ( 112-)  B 1    CB   6.10
1482 PHE   ( 112-)  B 1    CB   6.09
2167 PHE   ( 112-)  B 1    CB   6.09
1619 PHE   ( 112-)  B 1    CB   6.09
 249 PHE   ( 112-)  B      CB   6.08
1071 PHE   ( 112-)  B      CB   6.08
2030 PHE   ( 112-)  B 1    CB   6.08
 797 PHE   ( 112-)  B      CB   6.08
 386 PHE   ( 112-)  B      CB   6.07
 523 PHE   ( 112-)  B      CB   6.07
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -5.569

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 : -5.569

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -5.569
Model 2 : -5.561
Model 3 : -5.573
Model 4 : -5.586
Model 5 : -5.563
Model 6 : -5.562
Model 7 : -5.572
Model 8 : -5.581
Model 9 : -5.559
Model 10 : -5.550
Model 11 : -5.591
Model 12 : -5.562
Model 13 : -5.556
Model 14 : -5.571
Model 15 : -5.575
Model 16 : -5.574
Model 17 : -5.572
Model 18 : -5.569

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.

 293 THR   (  19-)  A    -3.1
 704 THR   (  19-)  A    -3.1
 978 THR   (  19-)  A    -3.1
 156 THR   (  19-)  A    -3.0
 567 THR   (  19-)  A    -3.0
1800 THR   (  19-)  A 1   -3.0
1252 THR   (  19-)  A 1   -3.0
2074 THR   (  19-)  A 1   -3.0
2348 THR   (  19-)  A 1   -3.0
 430 THR   (  19-)  A    -3.0
2211 THR   (  19-)  A 1   -3.0
 841 THR   (  19-)  A    -3.0
1937 THR   (  19-)  A 1   -3.0
1115 THR   (  19-)  A    -3.0
1389 THR   (  19-)  A 1   -3.0
1526 THR   (  19-)  A 1   -2.8
  19 THR   (  19-)  A    -2.8
1663 THR   (  19-)  A 1   -2.6
 246 GLU   ( 109-)  B    -2.5
 657 GLU   ( 109-)  B    -2.5
 520 GLU   ( 109-)  B    -2.5
2301 GLU   ( 109-)  B 1   -2.5
2164 GLU   ( 109-)  B 1   -2.5
 931 GLU   ( 109-)  B    -2.5
1890 GLU   ( 109-)  B 1   -2.5
And so on for a total of 220 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.

  19 THR   (  19-)  A  Poor phi/psi
  39 ASN   (  39-)  A  Poor phi/psi
  40 ASP   (  40-)  A  Poor phi/psi
  42 GLU   (  42-)  A  Poor phi/psi
  94 MET   (  94-)  B  Poor phi/psi
  96 LYS   (  96-)  B  Poor phi/psi
 107 LYS   ( 107-)  B  Poor phi/psi
 108 CYS   ( 108-)  B  Poor phi/psi
 109 GLU   ( 109-)  B  Poor phi/psi
 134 PHE   ( 134-)  B  Poor phi/psi
 156 THR   (  19-)  A  Poor phi/psi
 176 ASN   (  39-)  A  Poor phi/psi
 177 ASP   (  40-)  A  Poor phi/psi
 179 GLU   (  42-)  A  Poor phi/psi
 231 MET   (  94-)  B  Poor phi/psi
 233 LYS   (  96-)  B  Poor phi/psi
 244 LYS   ( 107-)  B  Poor phi/psi
 245 CYS   ( 108-)  B  Poor phi/psi
 246 GLU   ( 109-)  B  Poor phi/psi
 271 PHE   ( 134-)  B  Poor phi/psi
 293 THR   (  19-)  A  Poor phi/psi
 313 ASN   (  39-)  A  Poor phi/psi
 314 ASP   (  40-)  A  Poor phi/psi
 316 GLU   (  42-)  A  Poor phi/psi
 368 MET   (  94-)  B  Poor phi/psi
And so on for a total of 180 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.923

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -4.924
Model 2 : -4.580
Model 3 : -4.784
Model 4 : -4.656
Model 5 : -4.983
Model 6 : -5.257
Model 7 : -5.068
Model 8 : -5.227
Model 9 : -4.840
Model 10 : -5.041
Model 11 : -4.828
Model 12 : -5.026
Model 13 : -5.000
Model 14 : -4.642
Model 15 : -4.669
Model 16 : -5.397
Model 17 : -4.816
Model 18 : -4.871

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 SER   (   3-)  A      0
   4 ARG   (   4-)  A      0
   5 VAL   (   5-)  A      0
   6 LEU   (   6-)  A      0
  12 LEU   (  12-)  A      0
  13 TYR   (  13-)  A      0
  16 SER   (  16-)  A      0
  18 VAL   (  18-)  A      0
  19 THR   (  19-)  A      0
  20 GLU   (  20-)  A      0
  21 GLU   (  21-)  A      0
  27 LYS   (  27-)  A      0
  35 GLU   (  35-)  A      0
  36 LYS   (  36-)  A      0
  38 GLU   (  38-)  A      0
  39 ASN   (  39-)  A      0
  40 ASP   (  40-)  A      0
  41 PRO   (  41-)  A      0
  42 GLU   (  42-)  A      0
  43 TRP   (  43-)  A      0
  46 CYS   (  46-)  A      0
  50 ARG   (  50-)  A      0
  52 GLN   (  52-)  A      0
  60 TYR   (  60-)  A      0
  64 LEU   (  64-)  A      0
And so on for a total of 1446 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.205

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 1.239
Model 2 : 1.232
Model 3 : 1.229
Model 4 : 1.240
Model 5 : 1.232
Model 6 : 1.233
Model 7 : 1.225
Model 8 : 1.220
Model 9 : 1.238
Model 10 : 1.225
Model 11 : 1.229
Model 12 : 1.225
Model 13 : 1.236
Model 14 : 1.246
Model 15 : 1.239
Model 16 : 1.217
Model 17 : 1.230
Model 18 : 1.240

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]

  14 PRO   (  14-)  A    0.17 LOW
  37 PRO   (  37-)  A    0.14 LOW
  41 PRO   (  41-)  A    0.07 LOW
  57 PRO   (  57-)  A    0.08 LOW
  68 PRO   (  68-)  A    0.03 LOW
  77 PRO   (  77-)  B    0.10 LOW
  85 PRO   (  85-)  B    0.03 LOW
 111 PRO   ( 111-)  B    0.08 LOW
 151 PRO   (  14-)  A    0.17 LOW
 174 PRO   (  37-)  A    0.14 LOW
 178 PRO   (  41-)  A    0.07 LOW
 194 PRO   (  57-)  A    0.08 LOW
 205 PRO   (  68-)  A    0.03 LOW
 214 PRO   (  77-)  B    0.10 LOW
 222 PRO   (  85-)  B    0.03 LOW
 248 PRO   ( 111-)  B    0.08 LOW
 288 PRO   (  14-)  A    0.17 LOW
 311 PRO   (  37-)  A    0.14 LOW
 315 PRO   (  41-)  A    0.07 LOW
 331 PRO   (  57-)  A    0.08 LOW
 342 PRO   (  68-)  A    0.03 LOW
 351 PRO   (  77-)  B    0.10 LOW
 359 PRO   (  85-)  B    0.03 LOW
 385 PRO   ( 111-)  B    0.08 LOW
 425 PRO   (  14-)  A    0.17 LOW
And so on for a total of 144 lines.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. 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).

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

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

2377 ASN   (  48-)  A 1    N    <->  2381 GLN   (  52-)  A 1    O    0.52    2.18
1281 ASN   (  48-)  A 1    N    <->  1285 GLN   (  52-)  A 1    O    0.52    2.18
 459 ASN   (  48-)  A      N    <->   463 GLN   (  52-)  A      O    0.52    2.18
 596 ASN   (  48-)  A      N    <->   600 GLN   (  52-)  A      O    0.52    2.18
1966 ASN   (  48-)  A 1    N    <->  1970 GLN   (  52-)  A 1    O    0.52    2.18
1692 ASN   (  48-)  A 1    N    <->  1696 GLN   (  52-)  A 1    O    0.52    2.18
1829 ASN   (  48-)  A 1    N    <->  1833 GLN   (  52-)  A 1    O    0.52    2.18
1418 ASN   (  48-)  A 1    N    <->  1422 GLN   (  52-)  A 1    O    0.52    2.18
1144 ASN   (  48-)  A      N    <->  1148 GLN   (  52-)  A      O    0.52    2.18
1007 ASN   (  48-)  A      N    <->  1011 GLN   (  52-)  A      O    0.52    2.18
  48 ASN   (  48-)  A      N    <->    52 GLN   (  52-)  A      O    0.52    2.18
2103 ASN   (  48-)  A 1    N    <->  2107 GLN   (  52-)  A 1    O    0.52    2.18
1555 ASN   (  48-)  A 1    N    <->  1559 GLN   (  52-)  A 1    O    0.52    2.18
 322 ASN   (  48-)  A      N    <->   326 GLN   (  52-)  A      O    0.52    2.18
2240 ASN   (  48-)  A 1    N    <->  2244 GLN   (  52-)  A 1    O    0.52    2.18
 870 ASN   (  48-)  A      N    <->   874 GLN   (  52-)  A      O    0.52    2.18
 733 ASN   (  48-)  A      N    <->   737 GLN   (  52-)  A      O    0.52    2.18
 185 ASN   (  48-)  A      N    <->   189 GLN   (  52-)  A      O    0.52    2.18
1893 PHE   ( 112-)  B 1    CB   <->  1896 HIS   ( 115-)  B 1    C    0.46    2.74
1071 PHE   ( 112-)  B      CB   <->  1074 HIS   ( 115-)  B      C    0.46    2.74
1208 PHE   ( 112-)  B      CB   <->  1211 HIS   ( 115-)  B      C    0.46    2.74
 660 PHE   ( 112-)  B      CB   <->   663 HIS   ( 115-)  B      C    0.46    2.74
 249 PHE   ( 112-)  B      CB   <->   252 HIS   ( 115-)  B      C    0.46    2.74
2441 PHE   ( 112-)  B 1    CB   <->  2444 HIS   ( 115-)  B 1    C    0.46    2.74
1345 PHE   ( 112-)  B 1    CB   <->  1348 HIS   ( 115-)  B 1    C    0.46    2.74
And so on for a total of 2219 lines.

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck


















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 18

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Warning: Structural average packing environment a bit worrysome

Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: B; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: B; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: B; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: B; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: B; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: B; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: B; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: B; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: B; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: B; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: B; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: B; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: B; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: B; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: B; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: B; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: B; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: B; Model number 18

Note: Per-model averages for NQA


















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 18

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure