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 pdb1trl.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

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

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 VAL   ( 255-)  A    Zero
   2 VAL   ( 256-)  A    Zero
   3 GLY   ( 257-)  A    Zero
   4 ILE   ( 258-)  A    Zero
   5 GLY   ( 259-)  A    Zero
   6 ARG   ( 260-)  A    Zero
   7 ASP   ( 261-)  A    Zero
   8 LYS   ( 262-)  A    Zero
   9 LEU   ( 263-)  A    Zero
  10 GLY   ( 264-)  A    Zero
  11 LYS   ( 265-)  A    Zero
  12 ILE   ( 266-)  A    Zero
  13 PHE   ( 267-)  A    Zero
  14 TYR   ( 268-)  A    Zero
  15 ARG   ( 269-)  A    Zero
  16 ALA   ( 270-)  A    Zero
  17 LEU   ( 271-)  A    Zero
  18 THR   ( 272-)  A    Zero
  19 GLN   ( 273-)  A    Zero
  20 TYR   ( 274-)  A    Zero
  21 LEU   ( 275-)  A    Zero
  22 THR   ( 276-)  A    Zero
  23 PRO   ( 277-)  A    Zero
  24 THR   ( 278-)  A    Zero
  25 SER   ( 279-)  A    Zero
And so on for a total of 992 lines.

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.683
Model 2 : 0.685
Model 3 : 0.679
Model 4 : 0.671
Model 5 : 0.675
Model 6 : 0.668
Model 7 : 0.684
Model 8 : 0.708

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.

  13 PHE   ( 267-)  A      CA   CB   CG  106.81   -7.0
  72 GLY   ( 264-)  B     -C    N    CA  127.44    4.0
  75 PHE   ( 267-)  B      CA   CB   CG  107.98   -5.8
 137 PHE   ( 267-)  A      CA   CB   CG  107.82   -6.0
 199 PHE   ( 267-)  B      CA   CB   CG  108.32   -5.5
 216 LEU   ( 284-)  B      N    CA   CB  102.61   -4.6
 261 PHE   ( 267-)  A      CA   CB   CG  106.50   -7.3
 292 SER   ( 298-)  A      N    CA   C   123.47    4.4
 323 PHE   ( 267-)  B      CA   CB   CG  109.66   -4.1
 340 LEU   ( 284-)  B      N    CA   CB  103.48   -4.1
 385 PHE   ( 267-)  A      CA   CB   CG  109.14   -4.7
 387 ARG   ( 269-)  A      CB   CG   CD  105.66   -4.2
 387 ARG   ( 269-)  A      CG   CD   NE  103.64   -4.0
 419 GLN   ( 301-)  A      CG   CD   NE2  96.14  -13.5
 419 GLN   ( 301-)  A      CG   CD   OE1 142.31   10.8
 419 GLN   ( 301-)  A      NE2  CD   OE1 117.69   -4.9
 424 VAL   ( 306-)  A      C    CA   CB  117.95    4.1
 426 GLN   ( 308-)  A      NE2  CD   OE1 118.26   -4.3
 438 ILE   ( 258-)  B      N    CA   CB  117.80    4.3
 439 GLY   ( 259-)  B     -C    N    CA  129.02    5.0
 447 PHE   ( 267-)  B      CA   CB   CG  109.31   -4.5
 464 LEU   ( 284-)  B      N    CA   CB  102.24   -4.9
 465 ARG   ( 285-)  B      CG   CD   NE   99.29   -6.6
 465 ARG   ( 285-)  B      CD   NE   CZ  133.80    6.7
 483 VAL   ( 303-)  B      CG1  CB   CG2 100.89   -4.5
 488 GLN   ( 308-)  B      N    CA   CB  102.08   -5.0
 509 PHE   ( 267-)  A      CA   CB   CG  108.88   -4.9
 571 PHE   ( 267-)  B      CA   CB   CG  108.46   -5.3
 588 LEU   ( 284-)  B      N    CA   CB  101.39   -5.4
 612 GLN   ( 308-)  B      N    CA   CB  102.38   -4.8
 612 GLN   ( 308-)  B      CB   CG   CD  105.58   -4.1
 626 ARG   ( 260-)  A      CB   CG   CD  105.07   -4.5
 633 PHE   ( 267-)  A      CA   CB   CG  108.76   -5.0
 691 LEU   ( 263-)  B     -C    N    CA  129.53    4.3
 691 LEU   ( 263-)  B      N    CA   CB  102.76   -4.6
 695 PHE   ( 267-)  B      CA   CB   CG  106.45   -7.4
 757 PHE   ( 267-)  A      CA   CB   CG  108.17   -5.6
 800 PHE   ( 310-)  A      CA   CB   CG  109.04   -4.8
 819 PHE   ( 267-)  B      CA   CB   CG  106.90   -6.9
 832 ASN   ( 280-)  B      ND2  CG   OD1 115.39   -7.2
 835 GLN   ( 283-)  B      NE2  CD   OE1 118.58   -4.0
 875 ASP   ( 261-)  A      CA   CB   CG  117.38    4.8
 881 PHE   ( 267-)  A      CA   CB   CG  107.64   -6.2
 922 GLN   ( 308-)  A      NE2  CD   OE1 113.62   -9.0
 940 GLY   ( 264-)  B     -C    N    CA  127.70    4.2
 943 PHE   ( 267-)  B      CA   CB   CG  108.70   -5.1
 960 LEU   ( 284-)  B      N    CA   CB  102.35   -4.8

Note: Per-model averages for bond-angle check

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

Model 1 : 1.128
Model 2 : 1.147
Model 3 : 1.156
Model 4 : 1.293
Model 5 : 1.131
Model 6 : 1.150
Model 7 : 1.197
Model 8 : 1.133

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.

  55 ALA   ( 309-)  A      C      6.6    10.25     0.08
  59 VAL   ( 313-)  A      C      7.7    10.66     0.15
  69 ASP   ( 261-)  B      C      7.4    11.46    -0.01
 117 ALA   ( 309-)  B      C      6.9    10.63     0.08
 119 ASP   ( 311-)  B      C      6.1     9.41    -0.01
 121 VAL   ( 313-)  B      C     -6.6    -8.84     0.15
 125 VAL   ( 255-)  A      C     -6.9    -9.28     0.15
 128 ILE   ( 258-)  A      C     -8.3   -10.85     0.03
 141 LEU   ( 271-)  A      C      6.1     9.76     0.20
 179 ALA   ( 309-)  A      C      6.1     9.37     0.08
 188 VAL   ( 256-)  B      C     -6.5    -8.69     0.15
 218 ALA   ( 286-)  B      C      6.8    10.55     0.08
 228 TYR   ( 296-)  B      C     -6.2    -9.32     0.33
 229 GLY   ( 297-)  B      C      7.1     9.49     0.06
 234 GLU   ( 302-)  B      C      6.8     9.86    -0.03
 245 VAL   ( 313-)  B      C     -7.8   -10.55     0.15
 272 THR   ( 278-)  A      C     -7.6   -11.17     0.30
 273 SER   ( 279-)  A      C     -8.7   -13.94     0.37
 280 ALA   ( 286-)  A      C      6.1     9.34     0.08
 303 ALA   ( 309-)  A      C      6.7    10.39     0.08
 307 VAL   ( 313-)  A      C     -7.3    -9.80     0.15
 315 GLY   ( 259-)  B      C     14.0    18.58     0.06
 342 ALA   ( 286-)  B      C      6.8    10.42     0.08
 369 VAL   ( 313-)  B      C     -7.9   -10.64     0.15
 376 ILE   ( 258-)  A      C      8.9    11.71     0.03
And so on for a total of 62 lines.

Error: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals 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 2.5 worries us. 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 : 2.531

Note: Per-model averages for chirality check

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

Model 1 : 2.392
Model 2 : 2.599
Model 3 : 2.589
Model 4 : 2.802
Model 5 : 2.525
Model 6 : 2.475
Model 7 : 2.353
Model 8 : 2.483

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.

 292 SER   ( 298-)  A    4.52
 812 ARG   ( 260-)  B    4.51
 577 GLN   ( 273-)  B    4.42
 352 TYR   ( 296-)  B    4.35
 934 ILE   ( 258-)  B    4.29
  68 ARG   ( 260-)  B    4.26
 205 GLN   ( 273-)  B    4.14
 876 LYS   ( 262-)  A    4.05

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 : 1.505

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.

 922 GLN   ( 308-)  A   11.97
 419 GLN   ( 301-)  A   10.57
 398 ASN   ( 280-)  A    7.62
 543 GLN   ( 301-)  A    7.61
 391 GLN   ( 273-)  A    7.51
 460 ASN   ( 280-)  B    6.02
  26 ASN   ( 280-)  A    5.48
 860 GLN   ( 308-)  B    4.93
 295 GLN   ( 301-)  A    4.67
 825 GLN   ( 273-)  B    4.51
 503 ASP   ( 261-)  A    4.50
 612 GLN   ( 308-)  B    4.33
 894 ASN   ( 280-)  A    4.26
 887 GLN   ( 273-)  A    4.10

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.

 330 TYR   ( 274-)  B      OH  12.73
 166 TYR   ( 296-)  A      OH  11.29
 166 TYR   ( 296-)  A      CB  10.89
 634 TYR   ( 268-)  A      OH   9.75
  82 TYR   ( 274-)  B      OH   9.24
 724 TYR   ( 296-)  B      OH   9.17
 448 TYR   ( 268-)  B      OH   9.06
 476 TYR   ( 296-)  B      OH   8.63
 275 PHE   ( 281-)  A      CB   7.47
 510 TYR   ( 268-)  A      OH   7.06
  89 PHE   ( 281-)  B      CB   6.87
 826 TYR   ( 274-)  B      OH   6.81
 600 TYR   ( 296-)  B      OH   6.76
 385 PHE   ( 267-)  A      CB   6.57
 461 PHE   ( 281-)  B      CB   6.55
 337 PHE   ( 281-)  B      CB   6.51
 538 TYR   ( 296-)  A      OH   6.49
 647 PHE   ( 281-)  A      CB   6.42
 662 TYR   ( 296-)  A      OH   6.37
 392 TYR   ( 274-)  A      OH   6.37
 151 PHE   ( 281-)  A      CB   6.33
 138 TYR   ( 268-)  A      OH   6.24
 454 TYR   ( 274-)  B      OH   5.97
 262 TYR   ( 268-)  A      OH   5.93
 144 TYR   ( 274-)  A      OH   5.89
And so on for a total of 53 lines.

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 : -4.095

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.047
Model 2 : -4.276
Model 3 : -4.172
Model 4 : -3.950
Model 5 : -3.738
Model 6 : -4.514
Model 7 : -3.750
Model 8 : -4.312

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.

 209 PRO   ( 277-)  B    -2.8
 166 TYR   ( 296-)  A    -2.8
 891 PRO   ( 277-)  A    -2.5
 439 GLY   ( 259-)  B    -2.4
 396 THR   ( 278-)  A    -2.4
 940 GLY   ( 264-)  B    -2.4
 892 THR   ( 278-)  A    -2.4
 811 GLY   ( 259-)  B    -2.4
 271 PRO   ( 277-)  A    -2.3
  42 TYR   ( 296-)  A    -2.3
 123 VAL   ( 315-)  B    -2.3
 229 GLY   ( 297-)  B    -2.3
 148 THR   ( 278-)  A    -2.3
 479 THR   ( 299-)  B    -2.3
 247 VAL   ( 315-)  B    -2.3
 929 VAL   ( 315-)  A    -2.3
 878 GLY   ( 264-)  A    -2.3
 313 GLY   ( 257-)  B    -2.2
  65 GLY   ( 257-)  B    -2.2
  72 GLY   ( 264-)  B    -2.2
 499 GLY   ( 257-)  A    -2.2
 520 THR   ( 278-)  A    -2.2
 644 THR   ( 278-)  A    -2.2
 107 THR   ( 299-)  B    -2.1
  67 GLY   ( 259-)  B    -2.1
 374 VAL   ( 256-)  A    -2.1
 622 VAL   ( 256-)  A    -2.1
   2 VAL   ( 256-)  A    -2.1
 753 LEU   ( 263-)  A    -2.1
 334 THR   ( 278-)  B    -2.1
  66 ILE   ( 258-)  B    -2.1
 560 VAL   ( 256-)  B    -2.1
 506 GLY   ( 264-)  A    -2.1
 582 THR   ( 278-)  B    -2.0
 765 LEU   ( 275-)  A    -2.0
 768 THR   ( 278-)  A    -2.0
 872 ILE   ( 258-)  A    -2.0
 873 GLY   ( 259-)  A    -2.0
 688 ARG   ( 260-)  B    -2.0
 727 THR   ( 299-)  B    -2.0
 398 ASN   ( 280-)  A    -2.0
 691 LEU   ( 263-)  B    -2.0
 603 THR   ( 299-)  B    -2.0

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.

  17 LEU   ( 271-)  A  omega poor
  66 ILE   ( 258-)  B  Poor phi/psi
  68 ARG   ( 260-)  B  Poor phi/psi
  72 GLY   ( 264-)  B  Poor phi/psi
 130 ARG   ( 260-)  A  Poor phi/psi
 166 TYR   ( 296-)  A  Poor phi/psi
 168 SER   ( 298-)  A  omega poor
 169 THR   ( 299-)  A  Poor phi/psi
 229 GLY   ( 297-)  B  Poor phi/psi
 231 THR   ( 299-)  B  Poor phi/psi
 250 VAL   ( 256-)  A  omega poor
 254 ARG   ( 260-)  A  Poor phi/psi
 267 GLN   ( 273-)  A  omega poor
 292 SER   ( 298-)  A  Poor phi/psi
 293 THR   ( 299-)  A  Poor phi/psi, omega poor
 314 ILE   ( 258-)  B  Poor phi/psi
 391 GLN   ( 273-)  A  omega poor
 417 THR   ( 299-)  A  Poor phi/psi
 438 ILE   ( 258-)  B  Poor phi/psi
 439 GLY   ( 259-)  B  Poor phi/psi
 442 LYS   ( 262-)  B  omega poor
 459 SER   ( 279-)  B  omega poor
 479 THR   ( 299-)  B  Poor phi/psi, omega poor
 502 ARG   ( 260-)  A  Poor phi/psi
 506 GLY   ( 264-)  A  Poor phi/psi
 517 LEU   ( 275-)  A  omega poor
 562 ILE   ( 258-)  B  Poor phi/psi
 564 ARG   ( 260-)  B  Poor phi/psi
 603 THR   ( 299-)  B  Poor phi/psi
 626 ARG   ( 260-)  A  Poor phi/psi
 685 GLY   ( 257-)  B  Poor phi/psi
 686 ILE   ( 258-)  B  omega poor
 688 ARG   ( 260-)  B  Poor phi/psi
 701 GLN   ( 273-)  B  omega poor
 727 THR   ( 299-)  B  Poor phi/psi
 769 SER   ( 279-)  A  omega poor
 788 SER   ( 298-)  A  omega poor
 791 GLN   ( 301-)  A  omega poor
 804 GLY   ( 314-)  A  Poor phi/psi
 810 ILE   ( 258-)  B  Poor phi/psi
 811 GLY   ( 259-)  B  Poor phi/psi, omega poor
 825 GLN   ( 273-)  B  omega poor
 853 GLN   ( 301-)  B  omega poor
 873 GLY   ( 259-)  A  Poor phi/psi
 878 GLY   ( 264-)  A  Poor phi/psi
 913 THR   ( 299-)  A  Poor phi/psi
 934 ILE   ( 258-)  B  Poor phi/psi
 940 GLY   ( 264-)  B  Poor phi/psi
 974 SER   ( 298-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -4.386

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 : -4.386

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 : -4.167
Model 2 : -4.533
Model 3 : -4.508
Model 4 : -4.684
Model 5 : -3.878
Model 6 : -4.979
Model 7 : -4.931
Model 8 : -3.405

Warning: Unusual rotamers

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

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

 916 GLU   ( 302-)  A    0.37
 400 SER   ( 282-)  A    0.37
 547 SER   ( 305-)  A    0.37
 409 SER   ( 291-)  A    0.38
 423 SER   ( 305-)  A    0.38
 161 SER   ( 291-)  A    0.38
 276 SER   ( 282-)  A    0.38
 843 SER   ( 291-)  B    0.39
 719 SER   ( 291-)  B    0.40
 223 SER   ( 291-)  B    0.40

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!

   4 ILE   ( 258-)  A      0
  18 THR   ( 272-)  A      0
  20 TYR   ( 274-)  A      0
  24 THR   ( 278-)  A      0
  25 SER   ( 279-)  A      0
  42 TYR   ( 296-)  A      0
  61 VAL   ( 315-)  A      0
  62 LYS   ( 316-)  A      0
  63 VAL   ( 255-)  B      0
  64 VAL   ( 256-)  B      0
  66 ILE   ( 258-)  B      0
  68 ARG   ( 260-)  B      0
  80 THR   ( 272-)  B      0
  82 TYR   ( 274-)  B      0
  86 THR   ( 278-)  B      0
 104 TYR   ( 296-)  B      0
 109 GLN   ( 301-)  B      0
 120 ALA   ( 312-)  B      0
 121 VAL   ( 313-)  B      0
 123 VAL   ( 315-)  B      0
 124 LYS   ( 316-)  B      0
 125 VAL   ( 255-)  A      0
 126 VAL   ( 256-)  A      0
 128 ILE   ( 258-)  A      0
 130 ARG   ( 260-)  A      0
And so on for a total of 290 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 6.088
Model 2 : 6.471
Model 3 : 6.903
Model 4 : 6.719
Model 5 : 6.143
Model 6 : 6.514
Model 7 : 6.499
Model 8 : 5.753

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!

 809 GLY   ( 257-)  B   2.50   33
 253 GLY   ( 259-)  A   2.28   17
 370 GLY   ( 314-)  B   1.66   13

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]

  85 PRO   ( 277-)  B    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].

  23 PRO   ( 277-)  A    99.3 envelop C-beta (108 degrees)
 147 PRO   ( 277-)  A   106.6 envelop C-beta (108 degrees)
 209 PRO   ( 277-)  B   115.5 envelop C-beta (108 degrees)
 271 PRO   ( 277-)  A  -125.9 half-chair C-delta/C-gamma (-126 degrees)
 395 PRO   ( 277-)  A   120.5 half-chair C-beta/C-alpha (126 degrees)
 457 PRO   ( 277-)  B  -119.7 half-chair C-delta/C-gamma (-126 degrees)
 519 PRO   ( 277-)  A   102.5 envelop C-beta (108 degrees)
 581 PRO   ( 277-)  B  -118.9 half-chair C-delta/C-gamma (-126 degrees)
 767 PRO   ( 277-)  A   107.8 envelop C-beta (108 degrees)
 829 PRO   ( 277-)  B   101.1 envelop C-beta (108 degrees)
 891 PRO   ( 277-)  A  -134.4 half-chair C-delta/C-gamma (-126 degrees)
 953 PRO   ( 277-)  B   103.9 envelop C-beta (108 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.

 697 ARG   ( 269-)  B      CZ   <->   701 GLN   ( 273-)  B      NE2  0.19    2.91
 832 ASN   ( 280-)  B      OD1  <->   833 PHE   ( 281-)  B      N    0.05    2.55
 377 GLY   ( 259-)  A      CA   <->   378 ARG   ( 260-)  A      NH2  0.03    2.97
 163 THR   ( 293-)  A      O    <->   167 GLY   ( 297-)  A      N    0.01    2.69
 449 ARG   ( 269-)  B      CZ   <->   453 GLN   ( 273-)  B      NE2  0.01    3.09

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

Warning: Abnormal packing environment for some residues


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: 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

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