WHAT IF Check report

This file was created 2011-12-28 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 pdb1i8h.ent

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

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.

   7 TPO   (   7-)  A
  59 TPO   (   7-)  A
 111 TPO   (   7-)  A
 163 TPO   (   7-)  A
 215 TPO   (   7-)  A
 267 TPO   (   7-)  A
 319 TPO   (   7-)  A
 371 TPO   (   7-)  A
 423 TPO   (   7-)  A
 475 TPO   (   7-)  A 1

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 LYS   (   1-)  A    Zero
   2 VAL   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 VAL   (   4-)  A    Zero
   5 VAL   (   5-)  A    Zero
   6 ARG   (   6-)  A    Zero
   7 TPO   (   7-)  A    Zero
   8 PRO   (   8-)  A    Zero
   9 PRO   (   9-)  A    Zero
  10 LYS   (  10-)  A    Zero
  11 SER   (  11-)  A    Zero
  12 PRO   (  12-)  A    Zero
  13 SER   (  13-)  A    Zero
  14 LYS   (   1-)  B    Zero
  15 LEU   (   2-)  B    Zero
  16 PRO   (   3-)  B    Zero
  17 PRO   (   4-)  B    Zero
  18 GLY   (   5-)  B    Zero
  19 TRP   (   6-)  B    Zero
  20 GLU   (   7-)  B    Zero
  21 LYS   (   8-)  B    Zero
  22 ARG   (   9-)  B    Zero
  23 MET   (  10-)  B    Zero
  24 SER   (  11-)  B    Zero
  25 ARG   (  12-)  B    Zero
And so on for a total of 520 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.

 139 HIS   (  22-)  B      CG   CD2   1.40    4.2
 191 HIS   (  22-)  B      CG   CD2   1.40    4.2
 243 HIS   (  22-)  B      CG   CD2   1.41    4.5
 399 HIS   (  22-)  B      CG   CD2   1.40    4.0
 451 HIS   (  22-)  B      CG   CD2   1.40    4.4
 503 HIS   (  22-)  B 1    CG   CD2   1.40    4.2

Note: Per-model averages for bond-length check

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

Model 1 : 1.327
Model 2 : 1.364
Model 3 : 1.347
Model 4 : 1.351
Model 5 : 1.349
Model 6 : 1.337
Model 7 : 1.330
Model 8 : 1.365
Model 9 : 1.362
Model 10 : 1.371

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.

   8 PRO   (   8-)  A     -CA  -C    N   123.93    4.7
   8 PRO   (   8-)  A      C    CA   CB  118.24    4.3
   9 PRO   (   9-)  A     -CA  -C    N   123.99    4.7
   9 PRO   (   9-)  A      N    CA   CB   97.93   -4.6
   9 PRO   (   9-)  A      C    CA   CB  119.42    4.9
  14 LYS   (   1-)  B      C    CA   CB  117.95    4.1
  14 LYS   (   1-)  B      CA   CB   CG  122.20    4.1
  16 PRO   (   3-)  B      N    CA   C   121.96    4.1
  19 TRP   (   6-)  B      N    CA   CB  100.39   -5.9
  21 LYS   (   8-)  B      C    CA   CB  118.19    4.3
  25 ARG   (  12-)  B      CG   CD   NE  118.92    5.0
  30 VAL   (  17-)  B     -C    N    CA  129.24    4.2
  30 VAL   (  17-)  B      N    CA   CB  122.89    7.3
  30 VAL   (  17-)  B      C    CA   CB  119.74    5.1
  33 PHE   (  20-)  B      CA   CB   CG  118.63    4.8
  34 ASN   (  21-)  B      CA   CB   CG  119.01    6.4
  34 ASN   (  21-)  B      ND2  CG   OD1 117.54   -5.1
  35 HIS   (  22-)  B      CG   ND1  CE1 100.17   -5.4
  35 HIS   (  22-)  B      ND1  CE1  NE2 119.91    6.3
  35 HIS   (  22-)  B      CE1  NE2  CD2  98.68   -6.3
  35 HIS   (  22-)  B      NE2  CD2  CG  111.06    4.6
  35 HIS   (  22-)  B      CD2  CG   ND1 110.18    4.1
  42 TRP   (  29-)  B      C    CA   CB  118.61    4.5
  42 TRP   (  29-)  B      CA   CB   CG  121.90    4.4
  44 ARG   (  31-)  B      N    CA   CB   99.90   -6.2
And so on for a total of 213 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.745
Model 2 : 1.697
Model 3 : 1.719
Model 4 : 1.712
Model 5 : 1.691
Model 6 : 1.713
Model 7 : 1.830
Model 8 : 1.739
Model 9 : 1.729
Model 10 : 1.805

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.

  30 VAL   (  17-)  B      CA   -12.9    14.47    33.23
  82 VAL   (  17-)  B      CA   -10.5    17.95    33.23
 134 VAL   (  17-)  B      CA   -12.4    15.21    33.23
 160 VAL   (   4-)  A      CA    -6.9    23.27    33.23
 164 PRO   (   8-)  A      CA    -6.3    29.31    38.15
 186 VAL   (  17-)  B      CA   -11.3    16.82    33.23
 194 ASN   (  25-)  B      CA    -6.4    21.51    33.59
 238 VAL   (  17-)  B      CA    -7.9    21.75    33.23
 246 ASN   (  25-)  B      CA    -6.3    21.60    33.59
 262 VAL   (   2-)  A      CA    -8.1    21.44    33.23
 290 VAL   (  17-)  B      CA    -7.0    23.07    33.23
 342 VAL   (  17-)  B      CA   -13.4    13.80    33.23
 394 VAL   (  17-)  B      CA   -11.7    16.33    33.23
 446 VAL   (  17-)  B      CA   -13.1    14.21    33.23
 498 VAL   (  17-)  B 1    CA   -13.0    14.40    33.23
 512 ARG   (  31-)  B 1    CA    -6.6    23.14    33.91
The average deviation= 2.364

Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.0 worries us a bit. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.223

Note: Per-model averages for chirality check

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

Model 1 : 2.179
Model 2 : 2.170
Model 3 : 2.099
Model 4 : 2.360
Model 5 : 2.182
Model 6 : 2.055
Model 7 : 2.340
Model 8 : 2.100
Model 9 : 2.376
Model 10 : 2.337

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.

 324 PRO   (  12-)  A    4.33
 439 MET   (  10-)  B    4.06

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 : 1.541

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  77 ARG   (  12-)  B    6.48
 233 ARG   (  12-)  B    5.86
 435 TRP   (   6-)  B    4.24
 266 ARG   (   6-)  A    4.19
 509 GLN   (  28-)  B 1   4.06

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.

  31 TYR   (  18-)  B      CB  10.72
 499 TYR   (  18-)  B 1    CB  10.31
  83 TYR   (  18-)  B      CB   9.90
 447 TYR   (  18-)  B      CB   8.74
 395 TYR   (  18-)  B      CB   8.61
 291 TYR   (  18-)  B      CB   8.43
 343 TYR   (  18-)  B      CB   8.37
 239 TYR   (  18-)  B      CB   7.96
 187 TYR   (  18-)  B      CB   7.91
 135 TYR   (  18-)  B      CB   7.84
 383 TRP   (   6-)  B      CB   6.45
 198 TRP   (  29-)  B      CB   6.29
 499 TYR   (  18-)  B 1    OH   5.45
 302 TRP   (  29-)  B      CB   5.14
 188 TYR   (  19-)  B      CB   4.52
 347 HIS   (  22-)  B      CB   4.31
 239 TYR   (  18-)  B      OH   4.20
  83 TYR   (  18-)  B      OH   4.13
  87 HIS   (  22-)  B      CB   4.04
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -6.177

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 : -6.177

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.997
Model 2 : -5.529
Model 3 : -5.852
Model 4 : -7.058
Model 5 : -6.445
Model 6 : -6.331
Model 7 : -6.609
Model 8 : -5.505
Model 9 : -6.205
Model 10 : -6.238

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.

 324 PRO   (  12-)  A    -3.1
 135 TYR   (  18-)  B    -2.9
 187 TYR   (  18-)  B    -2.9
 499 TYR   (  18-)  B 1   -2.9
 327 LEU   (   2-)  B    -2.8
  83 TYR   (  18-)  B    -2.8
 431 LEU   (   2-)  B    -2.7
  67 LEU   (   2-)  B    -2.7
 171 LEU   (   2-)  B    -2.6
 447 TYR   (  18-)  B    -2.6
 337 ARG   (  12-)  B    -2.6
 246 ASN   (  25-)  B    -2.5
 239 TYR   (  18-)  B    -2.5
 214 ARG   (   6-)  A    -2.5
 478 LYS   (  10-)  A 1   -2.5
 202 SER   (  33-)  B    -2.4
 124 GLU   (   7-)  B    -2.4
 119 LEU   (   2-)  B    -2.4
 488 GLU   (   7-)  B 1   -2.4
 228 GLU   (   7-)  B    -2.4
  46 SER   (  33-)  B    -2.4
 280 GLU   (   7-)  B    -2.4
 176 GLU   (   7-)  B    -2.4
 194 ASN   (  25-)  B    -2.4
 232 SER   (  11-)  B    -2.4
And so on for a total of 68 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.

   3 SER   (   3-)  A  omega poor
   6 ARG   (   6-)  A  omega poor
   9 PRO   (   9-)  A  Poor phi/psi
  10 LYS   (  10-)  A  omega poor
  12 PRO   (  12-)  A  Poor phi/psi, omega poor
  19 TRP   (   6-)  B  omega poor
  23 MET   (  10-)  B  omega poor
  24 SER   (  11-)  B  Poor phi/psi, omega poor
  30 VAL   (  17-)  B  Poor phi/psi, omega poor
  31 TYR   (  18-)  B  omega poor
  38 ASN   (  25-)  B  Poor phi/psi
  43 GLU   (  30-)  B  omega poor
  45 PRO   (  32-)  B  Poor phi/psi
  46 SER   (  33-)  B  Poor phi/psi
  51 SER   (  38-)  B  omega poor
  57 VAL   (   5-)  A  Poor phi/psi
  61 PRO   (   9-)  A  Poor phi/psi
  62 LYS   (  10-)  A  omega poor
  67 LEU   (   2-)  B  Poor phi/psi
  69 PRO   (   4-)  B  omega poor
  71 TRP   (   6-)  B  omega poor
  74 ARG   (   9-)  B  omega poor
  75 MET   (  10-)  B  omega poor
  76 SER   (  11-)  B  Poor phi/psi
  78 SER   (  13-)  B  Poor phi/psi
And so on for a total of 215 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 : -5.862

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 : -5.355
Model 2 : -5.743
Model 3 : -5.785
Model 4 : -6.020
Model 5 : -6.007
Model 6 : -5.045
Model 7 : -5.243
Model 8 : -6.570
Model 9 : -6.697
Model 10 : -6.154

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!

   7 TPO   (   7-)  A      0
   9 PRO   (   9-)  A      0
  10 LYS   (  10-)  A      0
  12 PRO   (  12-)  A      0
  13 SER   (  13-)  A      0
  14 LYS   (   1-)  B      0
  15 LEU   (   2-)  B      0
  17 PRO   (   4-)  B      0
  19 TRP   (   6-)  B      0
  23 MET   (  10-)  B      0
  24 SER   (  11-)  B      0
  25 ARG   (  12-)  B      0
  26 SER   (  13-)  B      0
  27 SER   (  14-)  B      0
  29 ARG   (  16-)  B      0
  30 VAL   (  17-)  B      0
  31 TYR   (  18-)  B      0
  32 TYR   (  19-)  B      0
  35 HIS   (  22-)  B      0
  38 ASN   (  25-)  B      0
  40 SER   (  27-)  B      0
  42 TRP   (  29-)  B      0
  44 ARG   (  31-)  B      0
  46 SER   (  33-)  B      0
  48 ASN   (  35-)  B      0
And so on for a total of 414 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 : -2.488

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 : 16.595

Note: Per-model averages for omega angle check

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

Model 1 : 13.184
Model 2 : 15.662
Model 3 : 16.550
Model 4 : 14.913
Model 5 : 17.410
Model 6 : 17.399
Model 7 : 17.574
Model 8 : 16.564
Model 9 : 17.768
Model 10 : 18.244

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!

 278 GLY   (   5-)  B   1.53   40

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]

  45 PRO   (  32-)  B    0.17 LOW
 372 PRO   (   8-)  A    0.18 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].

   8 PRO   (   8-)  A  -119.6 half-chair C-delta/C-gamma (-126 degrees)
   9 PRO   (   9-)  A   -63.9 envelop C-beta (-72 degrees)
  69 PRO   (   4-)  B   -55.0 half-chair C-beta/C-alpha (-54 degrees)
 112 PRO   (   8-)  A   -11.5 half-chair C-alpha/N (-18 degrees)
 225 PRO   (   4-)  B   -65.8 envelop C-beta (-72 degrees)
 253 PRO   (  32-)  B  -115.6 envelop C-gamma (-108 degrees)
 277 PRO   (   4-)  B   -52.0 half-chair C-beta/C-alpha (-54 degrees)
 324 PRO   (  12-)  A   126.3 half-chair C-beta/C-alpha (126 degrees)
 381 PRO   (   4-)  B   -51.3 half-chair C-beta/C-alpha (-54 degrees)
 432 PRO   (   3-)  B    49.1 half-chair C-delta/C-gamma (54 degrees)
 485 PRO   (   4-)  B 1  -61.1 half-chair C-beta/C-alpha (-54 degrees)

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.

 475 TPO   (   7-)  A 1    O2P  <->   481 SER   (  13-)  A 1    O    1.01    1.39
 111 TPO   (   7-)  A      O1P  <->   117 SER   (  13-)  A      O    0.82    1.58
 319 TPO   (   7-)  A      O3P  <->   341 ARG   (  16-)  B      CB   0.79    2.01
 475 TPO   (   7-)  A 1    O2P  <->   481 SER   (  13-)  A 1    C    0.67    2.13
 111 TPO   (   7-)  A      O1P  <->   117 SER   (  13-)  A      C    0.61    2.19
 111 TPO   (   7-)  A      P    <->   525 SER   (  13-)  A      O''  0.49    2.51
 111 TPO   (   7-)  A      O3P  <->   525 SER   (  13-)  A      O''  0.46    1.94
 111 TPO   (   7-)  A      P    <->   117 SER   (  13-)  A      C    0.23    3.17
 475 TPO   (   7-)  A 1    P    <->   481 SER   (  13-)  A 1    O    0.21    2.79
 111 TPO   (   7-)  A      O1P  <->   525 SER   (  13-)  A      O''  0.19    2.21
 371 TPO   (   7-)  A      O2P  <->   377 SER   (  13-)  A      O    0.17    2.23
 319 TPO   (   7-)  A      O3P  <->   341 ARG   (  16-)  B      CG   0.17    2.63
 475 TPO   (   7-)  A 1    O2P  <->   539 SER   (  13-)  A 1    O''  0.12    2.28
 319 TPO   (   7-)  A      P    <->   337 ARG   (  12-)  B      NH2  0.11    3.19
  10 LYS   (  10-)  A      NZ   <->    13 SER   (  13-)  A      C    0.10    3.00
 371 TPO   (   7-)  A      P    <->   389 ARG   (  12-)  B      NH2  0.07    3.23
  62 LYS   (  10-)  A      NZ   <->    65 SER   (  13-)  A      C    0.06    3.04
 327 LEU   (   2-)  B      CD1  <->   331 TRP   (   6-)  B      CB   0.05    3.15
  72 GLU   (   7-)  B      OE2  <->    73 LYS   (   8-)  B      NZ   0.05    2.65
 267 TPO   (   7-)  A      O1P  <->   285 ARG   (  12-)  B      NH2  0.05    2.65
 118 LYS   (   1-)  B      NZ   <->   526 GLY   (  39-)  B      O''  0.05    2.65
 371 TPO   (   7-)  A      O2P  <->   377 SER   (  13-)  A      C    0.05    2.75
  20 GLU   (   7-)  B      OE2  <->    21 LYS   (   8-)  B      NZ   0.04    2.66
 228 GLU   (   7-)  B      OE2  <->   229 LYS   (   8-)  B      NZ   0.04    2.66
 481 SER   (  13-)  A 1    O    <->   493 ARG   (  12-)  B 1    NH2  0.04    2.66
 436 GLU   (   7-)  B      OE2  <->   437 LYS   (   8-)  B      NZ   0.04    2.66
 176 GLU   (   7-)  B      OE2  <->   177 LYS   (   8-)  B      NZ   0.04    2.66
 117 SER   (  13-)  A      C    <->   129 ARG   (  12-)  B      NH2  0.03    3.07
 124 GLU   (   7-)  B      OE2  <->   125 LYS   (   8-)  B      NZ   0.03    2.67
 488 GLU   (   7-)  B 1    OE2  <->   489 LYS   (   8-)  B 1    NZ   0.03    2.67
 270 LYS   (  10-)  A      NZ   <->   273 SER   (  13-)  A      O    0.03    2.67
  59 TPO   (   7-)  A      P    <->    77 ARG   (  12-)  B      NH2  0.03    3.27
 280 GLU   (   7-)  B      OE2  <->   281 LYS   (   8-)  B      NZ   0.03    2.67
 267 TPO   (   7-)  A      P    <->   285 ARG   (  12-)  B      NH2  0.02    3.28
 423 TPO   (   7-)  A      O1P  <->   441 ARG   (  12-)  B      NH2  0.01    2.69
 483 LEU   (   2-)  B 1    CD1  <->   487 TRP   (   6-)  B 1    CB   0.01    3.19

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

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Error: Abnormal average packing environment

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

Warning: Low packing Z-score for some residues


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

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: No crystallisation information

Final summary

Note: Summary report for users of a structure