WHAT IF Check report

This file was created 2012-01-30 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 pdb3cwu.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.821
CA-only RMS fit for the two chains : 0.499

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.947
CA-only RMS fit for the two chains : 0.569

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.914
CA-only RMS fit for the two chains : 0.552

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.764
CA-only RMS fit for the two chains : 0.403

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.744
CA-only RMS fit for the two chains : 0.394

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1179 2FE   (   8-)  E  -
1180 2FE   (   8-)  G  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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.

 282 ALA   ( 282-)  A    High
 563 GLU   ( 281-)  B    High
 845 GLU   ( 281-)  C    High
 846 ALA   ( 282-)  C    High
1136 DTHY  (   9-)  E    High
1137 DGUA  (  10-)  E    High
1138 DCYT  (  11-)  E    High
1139 DCYT  (  12-)  E    High
1145 DTHY  (  19-)  F    High
1146 DCYT  (  20-)  F    High
1147 DADE  (  21-)  F    High
1148 DTHY  (  22-)  F    High
1149 DGUA  (  23-)  F    High
1150 DTHY  (  24-)  F    High
1151 DCYT  (  25-)  F    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  56 ARG   (  56-)  A
  97 ARG   (  97-)  A
 379 ARG   (  97-)  B
 943 ARG   (  97-)  D

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

 284 TYR   (   2-)  B
 881 TYR   (  35-)  D
 988 TYR   ( 142-)  D

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 516 PHE   ( 234-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  32 ASP   (  32-)  A
  53 ASP   (  53-)  A
 280 ASP   ( 280-)  A
 314 ASP   (  32-)  B
 335 ASP   (  53-)  B
 596 ASP   (  32-)  C

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  73 GLU   (  73-)  A
 144 GLU   ( 144-)  A
 557 GLU   ( 275-)  B
 607 GLU   (  43-)  C
 744 GLU   ( 180-)  C
 767 GLU   ( 203-)  C
 822 GLU   ( 258-)  C
 914 GLU   (  68-)  D
 919 GLU   (  73-)  D
 997 GLU   ( 151-)  D
1026 GLU   ( 180-)  D

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.

1131 DCYT  (   3-)  E      O5'  C5'   1.37   -4.2
1132 DADE  (   4-)  E      O5'  C5'   1.38   -4.0
1134 DGUA  (   6-)  E      C5   C6    1.48    6.1
1136 DTHY  (   9-)  E      O5'  C5'   1.36   -4.8
1136 DTHY  (   9-)  E      C5'  C4'   1.48   -4.1
1137 DGUA  (  10-)  E      O5'  C5'   1.37   -4.6
1137 DGUA  (  10-)  E      C5'  C4'   1.48   -4.2
1140 DGUA  (  14-)  F      C5'  C4'   1.48   -4.1
1144 DTHY  (  18-)  F      C3'  O3'   1.38   -4.0
1144 DTHY  (  18-)  F      C5'  C4'   1.42  -11.3
1144 DTHY  (  18-)  F      C4'  C3'   1.59    6.3
1144 DTHY  (  18-)  F      N1   C6    1.41    5.3
1144 DTHY  (  18-)  F      N1   C2    1.43    6.8
1144 DTHY  (  18-)  F      C4   N3    1.42    4.7
1145 DTHY  (  19-)  F      C5'  C4'   1.45   -8.0
1146 DCYT  (  20-)  F      C5'  C4'   1.47   -5.6
1146 DCYT  (  20-)  F      N1   C2    1.44    4.0
1148 DTHY  (  22-)  F      O5'  C5'   1.36   -4.7
1148 DTHY  (  22-)  F      C5'  C4'   1.47   -5.1
1154 DCYT  (   3-)  G      O5'  C5'   1.37   -4.3
1155 DADE  (   4-)  G      O5'  C5'   1.36   -4.8
1155 DADE  (   4-)  G      C5'  C4'   1.47   -4.8
1156 DTHY  (   5-)  G      O5'  C5'   1.37   -4.5
1156 DTHY  (   5-)  G      C5'  C4'   1.48   -4.1
1157 DGUA  (   6-)  G      O5'  C5'   1.36   -4.7
1157 DGUA  (   6-)  G      C5'  C4'   1.47   -4.9
1158 DADE  (   7-)  G      O5'  C5'   1.37   -4.3
1158 DADE  (   7-)  G      C5'  C4'   1.47   -4.5
1160 DGUA  (  10-)  G      O5'  C5'   1.36   -5.2
1160 DGUA  (  10-)  G      C5'  C4'   1.46   -5.9
1163 DGUA  (  14-)  H      C5'  C4'   1.47   -4.7
1168 DTHY  (  19-)  H      O5'  C5'   1.38   -4.0
1170 DADE  (  21-)  H      O5'  C5'   1.37   -4.4
1171 DTHY  (  22-)  H      O5'  C5'   1.36   -5.0
1171 DTHY  (  22-)  H      C5'  C4'   1.45   -7.4
1173 DTHY  (  24-)  H      O5'  C5'   1.36   -4.9
1173 DTHY  (  24-)  H      C5'  C4'   1.47   -5.6

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.

1116 HIS   ( 270-)  D      CG   ND1  CE1 109.76    4.2
1129 DGUA  (   1-)  E      C3'  C4'  C5' 105.80   -5.9
1130 DADE  (   2-)  E      C3'  C4'  C5' 108.60   -4.1
1131 DCYT  (   3-)  E      C3'  C4'  C5' 108.45   -4.2
1132 DADE  (   4-)  E      C3'  C4'  C5' 106.68   -5.3
1133 DTHY  (   5-)  E      C3'  C4'  C5' 106.33   -5.6
1134 DGUA  (   6-)  E      C3'  C4'  C5' 106.11   -5.7
1135 DADE  (   7-)  E      C3'  C4'  C5' 107.44   -4.8
1136 DTHY  (   9-)  E      C3'  C4'  C5' 103.15   -7.7
1137 DGUA  (  10-)  E      C3'  C4'  C5' 103.72   -7.3
1137 DGUA  (  10-)  E      N9   C8   N7  113.46    4.7
1138 DCYT  (  11-)  E      C3'  C4'  C5' 106.87   -5.2
1139 DCYT  (  12-)  E      C3'  C4'  C5' 107.14   -5.0
1140 DGUA  (  14-)  F      C3'  C4'  C5' 107.02   -5.1
1141 DGUA  (  15-)  F      C3'  C4'  C5' 107.35   -4.9
1141 DGUA  (  15-)  F      N9   C8   N7  113.12    4.0
1143 DADE  (  17-)  F      C3'  C4'  C5' 107.30   -4.9
1143 DADE  (  17-)  F      C5'  C4'  O4' 116.06    4.2
1144 DTHY  (  18-)  F      C3'  C4'  C5' 106.50   -5.5
1145 DTHY  (  19-)  F      C3'  C4'  C5' 105.41   -6.2
1145 DTHY  (  19-)  F      N3   C2   O2  119.65   -4.4
1146 DCYT  (  20-)  F      C3'  C4'  C5' 107.56   -4.8
1146 DCYT  (  20-)  F      C5   C4   N4  123.16    4.2
1146 DCYT  (  20-)  F      N4   C4   N3  114.73   -4.7
1147 DADE  (  21-)  F      C3'  C4'  C5' 108.27   -4.3
And so on for a total of 56 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  32 ASP   (  32-)  A
  53 ASP   (  53-)  A
  56 ARG   (  56-)  A
  73 GLU   (  73-)  A
  97 ARG   (  97-)  A
 144 GLU   ( 144-)  A
 280 ASP   ( 280-)  A
 314 ASP   (  32-)  B
 335 ASP   (  53-)  B
 379 ARG   (  97-)  B
 557 GLU   ( 275-)  B
 596 ASP   (  32-)  C
 607 GLU   (  43-)  C
 744 GLU   ( 180-)  C
 767 GLU   ( 203-)  C
 822 GLU   ( 258-)  C
 914 GLU   (  68-)  D
 919 GLU   (  73-)  D
 943 ARG   (  97-)  D
 997 GLU   ( 151-)  D
1026 GLU   ( 180-)  D

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.

  90 ILE   (  90-)  A    7.17
1102 TYR   ( 256-)  D    5.06
 273 TYR   ( 273-)  A    4.64
  82 PHE   (  82-)  A    4.52
 979 LYS   ( 133-)  D    4.49
 980 LEU   ( 134-)  D    4.37
  45 ARG   (  45-)  A    4.27
  88 PRO   (  88-)  A    4.21
 473 GLU   ( 191-)  B    4.14
 141 LEU   ( 141-)  A    4.13
 252 GLN   ( 252-)  A    4.13
 377 LEU   (  95-)  B    4.12

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.396

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.

 826 PRO   ( 262-)  C    -3.1
 262 PRO   ( 262-)  A    -3.0
  57 HIS   (  57-)  A    -3.0
1120 THR   ( 274-)  D    -2.8
 689 LEU   ( 125-)  C    -2.8
1108 PRO   ( 262-)  D    -2.8
 814 PRO   ( 250-)  C    -2.7
 166 PRO   ( 166-)  A    -2.6
 849 THR   (   3-)  D    -2.5
 198 ILE   ( 198-)  A    -2.5
 407 LEU   ( 125-)  B    -2.4
 709 ARG   ( 145-)  C    -2.4
 557 GLU   ( 275-)  B    -2.4
1096 PRO   ( 250-)  D    -2.3
 380 LEU   (  98-)  B    -2.3
 544 PRO   ( 262-)  B    -2.3
 621 HIS   (  57-)  C    -2.3
 609 ARG   (  45-)  C    -2.2
 102 ARG   ( 102-)  A    -2.2
 150 PRO   ( 150-)  A    -2.2
1038 GLY   ( 192-)  D    -2.2
 990 GLU   ( 144-)  D    -2.2
 856 TYR   (  10-)  D    -2.2
1118 TRP   ( 272-)  D    -2.2
  96 GLY   (  96-)  A    -2.2
1077 LYS   ( 231-)  D    -2.1
  29 THR   (  29-)  A    -2.1
 889 GLU   (  43-)  D    -2.1
 957 VAL   ( 111-)  D    -2.1
 308 SER   (  26-)  B    -2.1
1085 TYR   ( 239-)  D    -2.1
  25 SER   (  25-)  A    -2.1
 904 THR   (  58-)  D    -2.1
 761 THR   ( 197-)  C    -2.1
 276 GLY   ( 276-)  A    -2.1
1101 ARG   ( 255-)  D    -2.1
 340 THR   (  58-)  B    -2.1
 972 VAL   ( 126-)  D    -2.0
 479 THR   ( 197-)  B    -2.0
1043 THR   ( 197-)  D    -2.0
 842 GLN   ( 278-)  C    -2.0
 375 GLY   (  93-)  B    -2.0
 250 PRO   ( 250-)  A    -2.0
 246 PRO   ( 246-)  A    -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.

   8 PRO   (   8-)  A  PRO omega poor
  26 SER   (  26-)  A  Poor phi/psi
  83 ASP   (  83-)  A  Poor phi/psi
  96 GLY   (  96-)  A  Poor phi/psi
  99 GLY   (  99-)  A  Poor phi/psi
 125 LEU   ( 125-)  A  Poor phi/psi
 173 GLY   ( 173-)  A  Poor phi/psi
 229 GLN   ( 229-)  A  Poor phi/psi
 261 LYS   ( 261-)  A  PRO omega poor
 275 GLU   ( 275-)  A  Poor phi/psi
 290 PRO   (   8-)  B  PRO omega poor
 308 SER   (  26-)  B  Poor phi/psi
 375 GLY   (  93-)  B  Poor phi/psi
 407 LEU   ( 125-)  B  Poor phi/psi
 543 LYS   ( 261-)  B  PRO omega poor
 557 GLU   ( 275-)  B  Poor phi/psi
 572 PRO   (   8-)  C  PRO omega poor
 590 SER   (  26-)  C  Poor phi/psi
 621 HIS   (  57-)  C  Poor phi/psi
 689 LEU   ( 125-)  C  Poor phi/psi
 764 GLY   ( 200-)  C  Poor phi/psi
 793 GLN   ( 229-)  C  Poor phi/psi
 803 TYR   ( 239-)  C  Poor phi/psi
 825 LYS   ( 261-)  C  PRO omega poor
 841 TRP   ( 277-)  C  Poor phi/psi
 845 GLU   ( 281-)  C  Poor phi/psi
 854 PRO   (   8-)  D  PRO omega poor
 872 SER   (  26-)  D  Poor phi/psi
 903 HIS   (  57-)  D  Poor phi/psi
 929 ASP   (  83-)  D  Poor phi/psi
1075 GLN   ( 229-)  D  Poor phi/psi
1107 LYS   ( 261-)  D  PRO omega poor
1119 TYR   ( 273-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.624

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.624

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 GLN   (   7-)  A      0
   8 PRO   (   8-)  A      0
  12 TRP   (  12-)  A      0
  22 ARG   (  22-)  A      0
  25 SER   (  25-)  A      0
  26 SER   (  26-)  A      0
  27 VAL   (  27-)  A      0
  31 ALA   (  31-)  A      0
  33 SER   (  33-)  A      0
  41 VAL   (  41-)  A      0
  43 GLU   (  43-)  A      0
  44 TYR   (  44-)  A      0
  45 ARG   (  45-)  A      0
  56 ARG   (  56-)  A      0
  57 HIS   (  57-)  A      0
  83 ASP   (  83-)  A      0
  86 CYS   (  86-)  A      0
  97 ARG   (  97-)  A      0
 102 ARG   ( 102-)  A      0
 110 CYS   ( 110-)  A      0
 111 VAL   ( 111-)  A      0
 124 GLN   ( 124-)  A      0
 125 LEU   ( 125-)  A      0
 126 VAL   ( 126-)  A      0
 142 TYR   ( 142-)  A      0
And so on for a total of 379 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 : 1.110

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!

 673 GLY   ( 109-)  C   1.90   10
 391 GLY   ( 109-)  B   1.86   11
1019 GLY   ( 173-)  D   1.74   33
 955 GLY   ( 109-)  D   1.72   13
 840 GLY   ( 276-)  C   1.63   55
 158 PRO   ( 158-)  A   1.57   16

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]

 826 PRO   ( 262-)  C    0.45 HIGH

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].

 250 PRO   ( 250-)  A   100.8 envelop C-beta (108 degrees)
 279 PRO   ( 279-)  A  -121.6 half-chair C-delta/C-gamma (-126 degrees)
 730 PRO   ( 166-)  C  -115.1 envelop C-gamma (-108 degrees)
 826 PRO   ( 262-)  C   -64.8 envelop C-beta (-72 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

1158 DADE  (   7-)  G      O3' <-> 1180 2FE   (   8-)  G      P      1.00    1.60  INTRA BF
1135 DADE  (   7-)  E      O3' <-> 1179 2FE   (   8-)  E      P      1.00    1.60  INTRA BF
1135 DADE  (   7-)  E      C3' <-> 1179 2FE   (   8-)  E      P      0.80    2.60  INTRA BF
1158 DADE  (   7-)  G      C3' <-> 1180 2FE   (   8-)  G      P      0.79    2.61  INTRA BF
1144 DTHY  (  18-)  F      N3  <-> 1179 2FE   (   8-)  E      C10    0.59    2.51  INTRA BF
 488 MET   ( 206-)  B      SD  <->  503 ASN   ( 221-)  B      ND2    0.36    2.94  INTRA BL
 889 GLU   (  43-)  D      OE2 <->  891 ARG   (  45-)  D      NH2    0.34    2.36  INTRA BF
 412 MET   ( 130-)  B      SD  <->  415 LYS   ( 133-)  B      NZ     0.34    2.96  INTRA BF
1155 DADE  (   4-)  G      N1  <-> 1171 DTHY  (  22-)  H      N3     0.31    2.69  INTRA BF
1167 DTHY  (  18-)  H      N3  <-> 1180 2FE   (   8-)  G      C10    0.31    2.79  INTRA
1170 DADE  (  21-)  H      C2' <-> 1171 DTHY  (  22-)  H      C5'    0.31    2.89  INTRA BF
1158 DADE  (   7-)  G      N1  <-> 1168 DTHY  (  19-)  H      N3     0.29    2.71  INTRA BF
 855 PRO   (   9-)  D      O   <->  952 ARG   ( 106-)  D      NH2    0.27    2.43  INTRA BL
 124 GLN   ( 124-)  A      NE2 <->  178 ARG   ( 178-)  A      NH1    0.27    2.58  INTRA BF
 379 ARG   (  97-)  B      O   <->  382 ALA   ( 100-)  B      N      0.27    2.43  INTRA BL
 391 GLY   ( 109-)  B      O   <->  508 ARG   ( 226-)  B      NH1    0.27    2.43  INTRA BL
 813 THR   ( 249-)  C      O   <->  816 GLN   ( 252-)  C      N      0.26    2.44  INTRA BF
 406 GLN   ( 124-)  B      OE1 <->  460 ARG   ( 178-)  B      NH1    0.26    2.44  INTRA BL
   3 THR   (   3-)  A      CG2 <->   60 HIS   (  60-)  A      ND1    0.26    2.84  INTRA BL
 244 ARG   ( 244-)  A      C   <->  246 PRO   ( 246-)  A      CD     0.26    2.94  INTRA BF
 673 GLY   ( 109-)  C      O   <->  790 ARG   ( 226-)  C      NH1    0.26    2.44  INTRA BL
 874 GLU   (  28-)  D      OE2 <->  965 ARG   ( 119-)  D      NH2    0.25    2.45  INTRA BF
 970 GLN   ( 124-)  D      NE2 <-> 1153 DADE  (   2-)  G      C5'    0.25    2.85  INTRA BF
 538 TYR   ( 256-)  B      CZ  <->  541 ARG   ( 259-)  B      NH1    0.24    2.86  INTRA BF
 914 GLU   (  68-)  D      N   <->  915 PRO   (  69-)  D      CD     0.24    2.76  INTRA BF
And so on for a total of 297 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 571 GLN   (   7-)  C      -6.83
 943 ARG   (  97-)  D      -6.73
 971 LEU   ( 125-)  D      -6.42
   7 GLN   (   7-)  A      -6.34
 289 GLN   (   7-)  B      -6.20
 853 GLN   (   7-)  D      -6.18
1127 GLU   ( 281-)  D      -6.04
 563 GLU   ( 281-)  B      -6.03
 281 GLU   ( 281-)  A      -5.73
 125 LEU   ( 125-)  A      -5.71
 845 GLU   ( 281-)  C      -5.64
 620 ARG   (  56-)  C      -5.63
 407 LEU   ( 125-)  B      -5.53
 102 ARG   ( 102-)  A      -5.53
 902 ARG   (  56-)  D      -5.32
 689 LEU   ( 125-)  C      -5.24
 666 ARG   ( 102-)  C      -5.24
  97 ARG   (  97-)  A      -5.19
 338 ARG   (  56-)  B      -5.14
  56 ARG   (  56-)  A      -5.12
 609 ARG   (  45-)  C      -5.05

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 541 ARG   ( 259-)  B       543 - LYS    261- ( B)         -4.19
 823 ARG   ( 259-)  C       825 - LYS    261- ( C)         -4.41

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  89 GLN   (  89-)  A
 124 GLN   ( 124-)  A
 187 ASN   ( 187-)  A
 469 ASN   ( 187-)  B
 525 GLN   ( 243-)  B
 688 GLN   ( 124-)  C
 704 GLN   ( 140-)  C

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  12 TRP   (  12-)  A      NE1
  14 TRP   (  14-)  A      NE1
  24 VAL   (  24-)  A      N
  45 ARG   (  45-)  A      NE
 106 ARG   ( 106-)  A      N
 106 ARG   ( 106-)  A      NE
 106 ARG   ( 106-)  A      NH1
 110 CYS   ( 110-)  A      N
 114 PHE   ( 114-)  A      N
 149 PHE   ( 149-)  A      N
 159 GLN   ( 159-)  A      N
 177 LYS   ( 177-)  A      N
 197 THR   ( 197-)  A      N
 229 GLN   ( 229-)  A      NE2
 234 PHE   ( 234-)  A      N
 235 LEU   ( 235-)  A      N
 294 TRP   (  12-)  B      NE1
 296 TRP   (  14-)  B      NE1
 345 LEU   (  63-)  B      N
 346 SER   (  64-)  B      OG
 388 ARG   ( 106-)  B      N
 388 ARG   ( 106-)  B      NE
 388 ARG   ( 106-)  B      NH1
 392 CYS   ( 110-)  B      N
 396 PHE   ( 114-)  B      N
And so on for a total of 77 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 270 HIS   ( 270-)  A      ND1
 350 GLU   (  68-)  B      OE2
 552 HIS   ( 270-)  B      ND1
 656 ASN   (  92-)  C      OD1
 834 HIS   ( 270-)  C      ND1
1116 HIS   ( 270-)  D      ND1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 151 GLU   ( 151-)  A   H-bonding suggests Gln
 462 GLU   ( 180-)  B   H-bonding suggests Gln
 914 GLU   (  68-)  D   H-bonding suggests Gln
1104 GLU   ( 258-)  D   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.861
  2nd generation packing quality :  -1.400
  Ramachandran plot appearance   :  -3.396 (poor)
  chi-1/chi-2 rotamer normality  :  -3.624 (poor)
  Backbone conformation          :   0.383

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.567 (tight)
  Bond angles                    :   0.760
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.243 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.409
  Inside/Outside distribution    :   0.968

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.567 (tight)
  Bond angles                    :   0.760
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.243 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.409
  Inside/Outside distribution    :   0.968
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.