WHAT IF Check report

This file was created 2012-01-25 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 pdb2kcf.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: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.565
Model 2 : 0.567
Model 3 : 0.576
Model 4 : 0.574
Model 5 : 0.569
Model 6 : 0.576
Model 7 : 0.581
Model 8 : 0.582
Model 9 : 0.561
Model 10 : 0.563
Model 11 : 0.575
Model 12 : 0.564
Model 13 : 0.581
Model 14 : 0.596
Model 15 : 0.576
Model 16 : 0.585
Model 17 : 0.587
Model 18 : 0.572
Model 19 : 0.579
Model 20 : 0.572

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.

   9 GLU   (   9-)  A     -C    N    CA  130.24    4.7
  17 GLY   (  17-)  A     -C    N    CA  127.72    4.2
  18 ARG   (  18-)  A     -C    N    CA  128.92    4.0
  19 VAL   (  19-)  A      C    CA   CB  120.63    5.5
  19 VAL   (  19-)  A      CA   CB   CG1 117.76    4.3
  40 LEU   (   4-)  A     -C    N    CA  129.05    4.1
  40 LEU   (   4-)  A      C    CA   CB  118.08    4.2
  47 ARG   (  11-)  A      CD   NE   CZ  129.03    4.1
  51 SER   (  15-)  A      C    CA   CB  118.26    4.3
  55 VAL   (  19-)  A      C    CA   CB  121.32    5.9
  55 VAL   (  19-)  A      CA   CB   CG1 117.30    4.0
  60 HIS   (  24-)  A      CA   CB   CG  118.23    4.4
  91 VAL   (  19-)  A      C    CA   CB  118.95    4.7
 119 ARG   (  11-)  A      CD   NE   CZ  129.19    4.2
 127 VAL   (  19-)  A      C    CA   CB  121.06    5.8
 131 ASN   (  23-)  A      CA   CB   CG  117.04    4.4
 132 HIS   (  24-)  A      CA   CB   CG  118.21    4.4
 163 VAL   (  19-)  A      C    CA   CB  119.82    5.1
 168 HIS   (  24-)  A      CA   CB   CG  117.99    4.2
 171 ASN   (  27-)  A     -C    N    CA  129.80    4.5
 199 VAL   (  19-)  A      C    CA   CB  120.55    5.5
 199 VAL   (  19-)  A      CA   CB   CG1 117.65    4.2
 203 ASN   (  23-)  A      CA   CB   CG  120.84    8.2
 203 ASN   (  23-)  A      ND2  CG   OD1 118.55   -4.0
 204 HIS   (  24-)  A      CA   CB   CG  119.58    5.8
And so on for a total of 90 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.346
Model 2 : 1.393
Model 3 : 1.340
Model 4 : 1.298
Model 5 : 1.289
Model 6 : 1.511
Model 7 : 1.352
Model 8 : 1.402
Model 9 : 1.348
Model 10 : 1.348
Model 11 : 1.388
Model 12 : 1.299
Model 13 : 1.372
Model 14 : 1.406
Model 15 : 1.499
Model 16 : 1.480
Model 17 : 1.367
Model 18 : 1.376
Model 19 : 1.486
Model 20 : 1.276

Note: Per-model averages for chirality check

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

Model 1 : 1.406
Model 2 : 1.439
Model 3 : 1.339
Model 4 : 1.356
Model 5 : 1.233
Model 6 : 1.396
Model 7 : 1.287
Model 8 : 1.423
Model 9 : 1.368
Model 10 : 1.437
Model 11 : 1.217
Model 12 : 1.235
Model 13 : 1.330
Model 14 : 1.450
Model 15 : 1.379
Model 16 : 1.327
Model 17 : 1.225
Model 18 : 1.299
Model 19 : 1.520
Model 20 : 1.246

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.

 312 HIS   (  24-)  A    5.47
  21 TYR   (  21-)  A    5.04
 527 ASN   (  23-)  A 1   5.00
 345 TYR   (  21-)  A 1   4.83
 273 TYR   (  21-)  A    4.79
 488 TYR   (  20-)  A 1   4.67
  44 TRP   (   8-)  A    4.56
 381 TYR   (  21-)  A 1   4.47
 633 TYR   (  21-)  A 1   4.31
  24 HIS   (  24-)  A    4.07
 672 HIS   (  24-)  A 1   4.05
 384 HIS   (  24-)  A 1   4.02

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.

 524 TYR   (  20-)  A 1    CB   6.46
 596 TYR   (  20-)  A 1    CB   5.89
 632 TYR   (  20-)  A 1    CB   5.62
 704 TYR   (  20-)  A 2    CB   4.93
 560 TYR   (  20-)  A 1    CB   4.84
 380 TYR   (  20-)  A 1    CB   4.62
  20 TYR   (  20-)  A      CB   4.44
 128 TYR   (  20-)  A      CB   4.15
 247 TRP   (  31-)  A      CB   4.04
 416 TYR   (  20-)  A 1    CB   4.01
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -5.382

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 : -5.382

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.343
Model 2 : -6.668
Model 3 : -4.992
Model 4 : -5.445
Model 5 : -4.020
Model 6 : -4.517
Model 7 : -5.206
Model 8 : -5.478
Model 9 : -4.779
Model 10 : -4.752
Model 11 : -5.420
Model 12 : -5.764
Model 13 : -4.146
Model 14 : -6.823
Model 15 : -4.596
Model 16 : -5.834
Model 17 : -6.723
Model 18 : -5.660
Model 19 : -6.459
Model 20 : -5.021

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.

 525 TYR   (  21-)  A 1   -3.6
 528 HIS   (  24-)  A 1   -2.8
 597 TYR   (  21-)  A 1   -2.8
 524 TYR   (  20-)  A 1   -2.8
  71 SER   (  35-)  A    -2.7
 302 ARG   (  14-)  A    -2.6
 304 SER   (  16-)  A    -2.6
  51 SER   (  15-)  A    -2.6
 632 TYR   (  20-)  A 1   -2.6
 375 SER   (  15-)  A 1   -2.6
 555 SER   (  15-)  A 1   -2.6
 719 SER   (  35-)  A 2   -2.6
 448 SER   (  16-)  A 1   -2.6
 256 LEU   (   4-)  A    -2.5
 668 TYR   (  20-)  A 1   -2.5
 398 SER   (   2-)  A 1   -2.5
 578 SER   (   2-)  A 1   -2.5
 231 SER   (  15-)  A    -2.5
  15 SER   (  15-)  A    -2.4
  17 GLY   (  17-)  A    -2.4
 554 ARG   (  14-)  A 1   -2.4
 452 TYR   (  20-)  A 1   -2.4
 526 PHE   (  22-)  A 1   -2.4
 633 TYR   (  21-)  A 1   -2.4
 466 PRO   (  34-)  A 1   -2.4
And so on for a total of 93 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 LYS   (   3-)  A  Poor phi/psi
   7 GLY   (   7-)  A  Poor phi/psi, omega poor
  13 SER   (  13-)  A  Poor phi/psi
  14 ARG   (  14-)  A  omega poor
  15 SER   (  15-)  A  Poor phi/psi
  17 GLY   (  17-)  A  Poor phi/psi
  27 ASN   (  27-)  A  Poor phi/psi, omega poor
  34 PRO   (  34-)  A  omega poor
  39 LYS   (   3-)  A  Poor phi/psi
  40 LEU   (   4-)  A  Poor phi/psi
  43 GLY   (   7-)  A  omega poor
  45 GLU   (   9-)  A  omega poor
  46 LYS   (  10-)  A  omega poor
  50 ARG   (  14-)  A  Poor phi/psi
  51 SER   (  15-)  A  Poor phi/psi
  55 VAL   (  19-)  A  omega poor
  70 PRO   (  34-)  A  Poor phi/psi
  74 SER   (   2-)  A  omega poor
  79 GLY   (   7-)  A  Poor phi/psi
  87 SER   (  15-)  A  omega poor
  88 SER   (  16-)  A  Poor phi/psi
  97 ILE   (  25-)  A  Poor phi/psi
  99 ASN   (  27-)  A  Poor phi/psi
 100 ALA   (  28-)  A  omega poor
 106 PRO   (  34-)  A  omega poor
And so on for a total of 181 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 : -5.695

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 : -6.620
Model 2 : -5.921
Model 3 : -4.735
Model 4 : -4.713
Model 5 : -6.069
Model 6 : -3.818
Model 7 : -7.912
Model 8 : -5.113
Model 9 : -6.927
Model 10 : -7.511
Model 11 : -4.311
Model 12 : -6.192
Model 13 : -6.052
Model 14 : -5.752
Model 15 : -5.999
Model 16 : -5.872
Model 17 : -5.571
Model 18 : -5.471
Model 19 : -5.938
Model 20 : -3.395

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 LYS   (   3-)  A      0
   6 PRO   (   6-)  A      0
   8 TRP   (   8-)  A      0
   9 GLU   (   9-)  A      0
  13 SER   (  13-)  A      0
  14 ARG   (  14-)  A      0
  15 SER   (  15-)  A      0
  18 ARG   (  18-)  A      0
  19 VAL   (  19-)  A      0
  20 TYR   (  20-)  A      0
  21 TYR   (  21-)  A      0
  24 HIS   (  24-)  A      0
  28 ALA   (  28-)  A      0
  29 SER   (  29-)  A      0
  30 GLN   (  30-)  A      0
  31 TRP   (  31-)  A      0
  32 GLU   (  32-)  A      0
  34 PRO   (  34-)  A      0
  35 SER   (  35-)  A      0
  36 GLY   (  36-)  A      0
  37 GLY   (   1-)  A      0
  38 SER   (   2-)  A      0
  39 LYS   (   3-)  A      0
  40 LEU   (   4-)  A      0
  42 PRO   (   6-)  A      0
And so on for a total of 557 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 : -2.919

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 : 10.680

Note: Per-model averages for omega angle check

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

Model 1 : 9.712
Model 2 : 10.779
Model 3 : 9.523
Model 4 : 9.520
Model 5 : 9.225
Model 6 : 11.154
Model 7 : 11.548
Model 8 : 10.715
Model 9 : 11.961
Model 10 : 10.678
Model 11 : 8.779
Model 12 : 11.399
Model 13 : 10.958
Model 14 : 10.763
Model 15 : 11.297
Model 16 : 11.706
Model 17 : 11.957
Model 18 : 10.187
Model 19 : 10.668
Model 20 : 10.195

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!

 413 GLY   (  17-)  A 1  2.56   13
 593 GLY   (  17-)  A 1  1.55   80

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]

  70 PRO   (  34-)  A    0.13 LOW
  77 PRO   (   5-)  A    0.19 LOW
 106 PRO   (  34-)  A    0.18 LOW
 149 PRO   (   5-)  A    0.20 LOW
 178 PRO   (  34-)  A    0.06 LOW
 250 PRO   (  34-)  A    0.05 LOW
 286 PRO   (  34-)  A    0.08 LOW
 293 PRO   (   5-)  A    0.14 LOW
 322 PRO   (  34-)  A    0.20 LOW
 358 PRO   (  34-)  A 1   0.05 LOW
 430 PRO   (  34-)  A 1   0.10 LOW
 466 PRO   (  34-)  A 1   0.20 LOW
 502 PRO   (  34-)  A 1   0.15 LOW
 610 PRO   (  34-)  A 1   0.17 LOW
 646 PRO   (  34-)  A 1   0.17 LOW
 682 PRO   (  34-)  A 1   0.08 LOW
 689 PRO   (   5-)  A 2   0.11 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].

   5 PRO   (   5-)  A   -46.1 half-chair C-beta/C-alpha (-54 degrees)
  34 PRO   (  34-)  A   -65.9 envelop C-beta (-72 degrees)
  41 PRO   (   5-)  A   -63.3 envelop C-beta (-72 degrees)
 214 PRO   (  34-)  A   -58.5 half-chair C-beta/C-alpha (-54 degrees)
 257 PRO   (   5-)  A   -62.2 half-chair C-beta/C-alpha (-54 degrees)
 401 PRO   (   5-)  A 1   51.1 half-chair C-delta/C-gamma (54 degrees)
 437 PRO   (   5-)  A 1  -65.3 envelop C-beta (-72 degrees)
 509 PRO   (   5-)  A 1  -62.8 half-chair C-beta/C-alpha (-54 degrees)
 545 PRO   (   5-)  A 1  -64.6 envelop C-beta (-72 degrees)
 574 PRO   (  34-)  A 1  -42.6 envelop C-alpha (-36 degrees)
 581 PRO   (   5-)  A 1  -65.0 envelop C-beta (-72 degrees)
 617 PRO   (   5-)  A 1  -55.3 half-chair C-beta/C-alpha (-54 degrees)
 653 PRO   (   5-)  A 1  -38.7 envelop C-alpha (-36 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. 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).

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.

 547 GLY   (   7-)  A 1    C   <->  564 HIS   (  24-)  A 1    CE1    0.21    2.99
 691 GLY   (   7-)  A 2    C   <->  708 HIS   (  24-)  A 2    CE1    0.16    3.04
 406 LYS   (  10-)  A 1    CE  <->  417 TYR   (  21-)  A 1    CE2    0.15    3.05
 527 ASN   (  23-)  A 1    CG  <->  528 HIS   (  24-)  A 1    N      0.14    2.86
 276 HIS   (  24-)  A      CE1 <->  277 ILE   (  25-)  A      CD1    0.13    3.07
 367 GLY   (   7-)  A 1    C   <->  384 HIS   (  24-)  A 1    CE1    0.12    3.08
 187 GLY   (   7-)  A      C   <->  204 HIS   (  24-)  A      CE1    0.12    3.08
 272 TYR   (  20-)  A      CD2 <->  281 SER   (  29-)  A      CB     0.12    3.08
 619 GLY   (   7-)  A 1    C   <->  636 HIS   (  24-)  A 1    CE1    0.12    3.08
 154 LYS   (  10-)  A      CE  <->  165 TYR   (  21-)  A      CE2    0.12    3.08
 259 GLY   (   7-)  A      CA  <->  276 HIS   (  24-)  A      CE1    0.11    3.09
 548 TRP   (   8-)  A 1    CE3 <->  563 ASN   (  23-)  A 1    N      0.11    2.99
 475 GLY   (   7-)  A 1    C   <->  492 HIS   (  24-)  A 1    CE1    0.11    3.09
 439 GLY   (   7-)  A 1    CA  <->  456 HIS   (  24-)  A 1    CE1    0.10    3.10
  76 LEU   (   4-)  A      CD2 <->   80 TRP   (   8-)  A      CE2    0.10    3.10
 151 GLY   (   7-)  A      C   <->  168 HIS   (  24-)  A      CE1    0.10    3.10
 583 GLY   (   7-)  A 1    C   <->  600 HIS   (  24-)  A 1    CE1    0.10    3.10
 476 TRP   (   8-)  A 1    CE3 <->  491 ASN   (  23-)  A 1    N      0.10    3.00
 226 LYS   (  10-)  A      CE  <->  237 TYR   (  21-)  A      CE2    0.09    3.11
 416 TYR   (  20-)  A 1    CD2 <->  425 SER   (  29-)  A 1    CB     0.09    3.11
 292 LEU   (   4-)  A      CD2 <->  296 TRP   (   8-)  A      CZ2    0.09    3.11
 456 HIS   (  24-)  A 1    CE1 <->  457 ILE   (  25-)  A 1    CD1    0.09    3.11
 308 TYR   (  20-)  A      CE2 <->  317 SER   (  29-)  A      CB     0.08    3.12
 400 LEU   (   4-)  A 1    CD1 <->  428 GLU   (  32-)  A 1    C      0.08    3.12
 584 TRP   (   8-)  A 1    CE2 <->  599 ASN   (  23-)  A 1    ND2    0.08    3.02
And so on for a total of 74 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: A; 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: A; 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: A; 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: A; 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: A; 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: A; 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: A; 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: A; 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: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

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: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

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: A; 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: A; 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: A; 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: A; 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: A; 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: A; 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: A; 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: A; 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: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure