WHAT IF Check report

This file was created 2011-12-16 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 pdb2ixp.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 D

All-atom RMS fit for the two chains : 0.638
CA-only RMS fit for the two chains : 0.341

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 : 0.619
CA-only RMS fit for the two chains : 0.320

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: F and G

All-atom RMS fit for the two chains : 0.381
CA-only RMS fit for the two chains : 0.125

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: F and H

All-atom RMS fit for the two chains : 0.840
CA-only RMS fit for the two chains : 0.291

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: F and I

All-atom RMS fit for the two chains : 0.389
CA-only RMS fit for the two chains : 0.126

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.

1269 SIN   (   1-)  G  -
1270 NIT   (   6-)  G  -
1271 SIN   (   1-)  H  -
1272 NIT   (   6-)  H  -
1273 SIN   (   1-)  I  -
1274 NIT   (   6-)  I  -
1281 SIN   (   1-)  F  -
1282 NIT   (   6-)  F  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1253 ALA   (   2-)  F  -   N   bound to 1281 SIN   (   1-)  F  -   C4
1257 ALA   (   2-)  G  -   N   bound to 1269 SIN   (   1-)  G  -   C4
1261 ALA   (   2-)  H  -   N   bound to 1271 SIN   (   1-)  H  -   C4
1265 ALA   (   2-)  I  -   N   bound to 1273 SIN   (   1-)  I  -   C4

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: 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 4

Crystal temperature (K) :100.000

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.048

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 98.24

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: Tyrosine convention problem

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

  44 TYR   (  45-)  A
 114 TYR   ( 121-)  A
 124 TYR   ( 131-)  A
 174 TYR   ( 181-)  A
 184 TYR   ( 191-)  A
 205 TYR   ( 212-)  A
 235 TYR   ( 242-)  A
 241 TYR   ( 248-)  A
 354 TYR   (  45-)  B
 402 TYR   (  93-)  B
 430 TYR   ( 121-)  B
 440 TYR   ( 131-)  B
 453 TYR   ( 144-)  B
 490 TYR   ( 181-)  B
 500 TYR   ( 191-)  B
 521 TYR   ( 212-)  B
 557 TYR   ( 248-)  B
 580 TYR   ( 271-)  B
 665 TYR   (  40-)  C
 670 TYR   (  45-)  C
 718 TYR   (  93-)  C
 756 TYR   ( 131-)  C
 806 TYR   ( 181-)  C
 816 TYR   ( 191-)  C
 837 TYR   ( 212-)  C
 867 TYR   ( 242-)  C
 873 TYR   ( 248-)  C
 896 TYR   ( 271-)  C
 986 TYR   (  45-)  D
1056 TYR   ( 121-)  D
1066 TYR   ( 131-)  D
1116 TYR   ( 181-)  D
1126 TYR   ( 191-)  D
1147 TYR   ( 212-)  D
1177 TYR   ( 242-)  D
1183 TYR   ( 248-)  D

Warning: Phenylalanine convention problem

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

  12 PHE   (  13-)  A
  20 PHE   (  21-)  A
 158 PHE   ( 165-)  A
 201 PHE   ( 208-)  A
 240 PHE   ( 247-)  A
 256 PHE   ( 263-)  A
 298 PHE   ( 305-)  A
 304 PHE   ( 311-)  A
 305 PHE   ( 312-)  A
 330 PHE   (  21-)  B
 474 PHE   ( 165-)  B
 517 PHE   ( 208-)  B
 556 PHE   ( 247-)  B
 620 PHE   ( 311-)  B
 621 PHE   ( 312-)  B
 646 PHE   (  21-)  C
 761 PHE   ( 136-)  C
 790 PHE   ( 165-)  C
 833 PHE   ( 208-)  C
 872 PHE   ( 247-)  C
 936 PHE   ( 311-)  C
 937 PHE   ( 312-)  C
 954 PHE   (  13-)  D
1071 PHE   ( 136-)  D
1100 PHE   ( 165-)  D
1109 PHE   ( 174-)  D
1112 PHE   ( 177-)  D
1143 PHE   ( 208-)  D
1182 PHE   ( 247-)  D
1198 PHE   ( 263-)  D
1242 PHE   ( 307-)  D
1246 PHE   ( 311-)  D
1247 PHE   ( 312-)  D

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.

   6 ASP   (   7-)  A
  21 ASP   (  22-)  A
  81 ASP   (  82-)  A
 136 ASP   ( 143-)  A
 198 ASP   ( 205-)  A
 237 ASP   ( 244-)  A
 265 ASP   ( 272-)  A
 313 ASP   (   4-)  B
 331 ASP   (  22-)  B
 391 ASP   (  82-)  B
 452 ASP   ( 143-)  B
 514 ASP   ( 205-)  B
 581 ASP   ( 272-)  B
 632 ASP   (   7-)  C
 647 ASP   (  22-)  C
 707 ASP   (  82-)  C
 768 ASP   ( 143-)  C
 830 ASP   ( 205-)  C
 897 ASP   ( 272-)  C
 948 ASP   (   7-)  D
 963 ASP   (  22-)  D
1023 ASP   (  82-)  D
1078 ASP   ( 143-)  D
1140 ASP   ( 205-)  D
1207 ASP   ( 272-)  D

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.

  93 GLU   ( 100-)  A
 120 GLU   ( 127-)  A
 234 GLU   ( 241-)  A
 258 GLU   ( 265-)  A
 287 GLU   ( 294-)  A
 409 GLU   ( 100-)  B
 416 GLU   ( 107-)  B
 432 GLU   ( 123-)  B
 603 GLU   ( 294-)  B
 725 GLU   ( 100-)  C
 732 GLU   ( 107-)  C
 748 GLU   ( 123-)  C
 774 GLU   ( 149-)  C
 857 GLU   ( 232-)  C
 919 GLU   ( 294-)  C
1035 GLU   ( 100-)  D
1176 GLU   ( 241-)  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.

  85 PRO   (  86-)  A      N    CA    1.53    4.0
 149 VAL   ( 156-)  A      CA   CB    1.61    4.1
 178 ARG   ( 185-)  A      CB   CG    1.74    7.5
 178 ARG   ( 185-)  A      CG   CD    1.67    5.0
 226 ILE   ( 233-)  A      CG1  CD1   1.77    6.5
 400 ARG   (  91-)  B      CB   CG    1.65    4.2
 400 ARG   (  91-)  B      CG   CD    1.65    4.4
 564 ILE   ( 255-)  B      CA   CB    1.61    4.1
 679 ASP   (  54-)  C      CG   OD2   1.34    4.7
 723 CYS   (  98-)  C      CB   SG    1.67   -4.3
 780 THR   ( 155-)  C      CA   CB    1.62    4.3
 819 GLU   ( 194-)  C      CG   CD    1.65    5.4
 861 LYS   ( 236-)  C      CB   CG    1.65    4.5
 861 LYS   ( 236-)  C      CG   CD    1.66    4.6
 861 LYS   ( 236-)  C      CD   CE    1.66    4.6
 940 VAL   ( 315-)  C      CA   CB    1.62    4.7
1031 LEU   (  96-)  D      CA   C     1.62    4.5
1120 ARG   ( 185-)  D      CB   CG    1.67    5.1
1120 ARG   ( 185-)  D      CG   CD    1.66    4.5
1129 GLU   ( 194-)  D      CG   CD    1.62    4.2
1189 PHE   ( 254-)  D      CB   CG    1.41   -4.2
1260 LYS   (   5-)  G      C    O     1.44   10.5
1264 LYS   (   5-)  H      C    O     1.40    8.5
1268 LYS   (   5-)  I      CA   C     1.68    7.2
1268 LYS   (   5-)  I      C    O     1.45   11.0

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998360 -0.000176 -0.000076|
 | -0.000176  0.998977  0.000224|
 | -0.000076  0.000224  0.999402|
Proposed new scale matrix

 |  0.011529  0.006654  0.000000|
 |  0.000002  0.013304 -0.000003|
 |  0.000000  0.000000  0.002436|
With corresponding cell

    A    =  86.746  B   =  86.797  C    = 410.432
    Alpha=  89.986  Beta=  90.010  Gamma= 120.001

The CRYST1 cell dimensions

    A    =  86.889  B   =  86.886  C    = 410.678
    Alpha=  90.000  Beta=  90.000  Gamma= 120.001

Variance: 56.712
(Under-)estimated Z-score: 5.550

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 HIS   (  10-)  A      CG   ND1  CE1 109.67    4.1
  26 LEU   (  27-)  A      C    CA   CB  120.48    5.5
  50 HIS   (  51-)  A      CG   ND1  CE1 110.51    4.9
  66 VAL   (  67-)  A     -C    N    CA  113.28   -4.7
  66 VAL   (  67-)  A      N    CA   CB  117.38    4.0
  78 HIS   (  79-)  A      CG   ND1  CE1 109.70    4.1
  85 PRO   (  86-)  A      N    CA   C   122.02    4.1
  88 ASN   (  95-)  A      N    CA   C   122.94    4.2
  89 LEU   (  96-)  A      N    CA   C   123.00    4.2
 115 HIS   ( 122-)  A      CG   ND1  CE1 109.60    4.0
 166 VAL   ( 173-)  A      N    CA   CB  118.31    4.6
 185 THR   ( 192-)  A      C    CA   CB  118.34    4.3
 200 HIS   ( 207-)  A      CG   ND1  CE1 109.76    4.2
 202 HIS   ( 209-)  A      CG   ND1  CE1 109.92    4.3
 204 VAL   ( 211-)  A      N    CA   C    98.04   -4.7
 238 THR   ( 245-)  A      C    CA   CB  121.55    6.0
 238 THR   ( 245-)  A      CA   CB   CG2 118.60    4.8
 308 VAL   ( 315-)  A      C    CA   CB  118.16    4.2
 319 HIS   (  10-)  B      CG   ND1  CE1 109.75    4.1
 326 VAL   (  17-)  B      C    CA   CB  118.12    4.2
 345 HIS   (  36-)  B      CG   ND1  CE1 110.06    4.5
 346 ARG   (  37-)  B      CG   CD   NE  103.12   -4.3
 360 HIS   (  51-)  B      CG   ND1  CE1 109.86    4.3
 369 THR   (  60-)  B      C    CA   CB  118.11    4.2
 375 MET   (  66-)  B     -C    N    CA  114.28   -4.1
And so on for a total of 102 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.

   6 ASP   (   7-)  A
  21 ASP   (  22-)  A
  81 ASP   (  82-)  A
  93 GLU   ( 100-)  A
 120 GLU   ( 127-)  A
 136 ASP   ( 143-)  A
 198 ASP   ( 205-)  A
 234 GLU   ( 241-)  A
 237 ASP   ( 244-)  A
 258 GLU   ( 265-)  A
 265 ASP   ( 272-)  A
 287 GLU   ( 294-)  A
 313 ASP   (   4-)  B
 331 ASP   (  22-)  B
 391 ASP   (  82-)  B
 409 GLU   ( 100-)  B
 416 GLU   ( 107-)  B
 432 GLU   ( 123-)  B
 452 ASP   ( 143-)  B
 514 ASP   ( 205-)  B
 581 ASP   ( 272-)  B
 603 GLU   ( 294-)  B
 632 ASP   (   7-)  C
 647 ASP   (  22-)  C
 707 ASP   (  82-)  C
 725 GLU   ( 100-)  C
 732 GLU   ( 107-)  C
 748 GLU   ( 123-)  C
 768 ASP   ( 143-)  C
 774 GLU   ( 149-)  C
 830 ASP   ( 205-)  C
 857 GLU   ( 232-)  C
 897 ASP   ( 272-)  C
 919 GLU   ( 294-)  C
 948 ASP   (   7-)  D
 963 ASP   (  22-)  D
1023 ASP   (  82-)  D
1035 GLU   ( 100-)  D
1078 ASP   ( 143-)  D
1140 ASP   ( 205-)  D
1176 GLU   ( 241-)  D
1207 ASP   ( 272-)  D

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  26 LEU   (  27-)  A      CA    -7.9    22.04    34.19
  66 VAL   (  67-)  A      CA    -6.9    23.16    33.23
 248 ILE   ( 255-)  A      CB     6.1    40.21    32.31
 566 GLU   ( 257-)  B      CA    -6.9    22.59    33.96
 604 VAL   ( 295-)  B      CA    -8.2    21.29    33.23
 847 LEU   ( 222-)  C      CA    -7.2    23.14    34.19
1091 VAL   ( 156-)  D      CA   -10.8    17.60    33.23
1230 VAL   ( 295-)  D      CA    -6.4    23.97    33.23
1268 LYS   (   5-)  I      CA    -6.3    23.40    33.92
The average deviation= 1.493

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.

 204 VAL   ( 211-)  A    8.26
1049 GLN   ( 114-)  D    6.89
 458 GLU   ( 149-)  B    6.56
 862 SER   ( 237-)  C    6.43
 883 VAL   ( 258-)  C    6.18
 441 LEU   ( 132-)  B    6.11
1019 ALA   (  78-)  D    6.08
  92 ARG   (  99-)  A    6.01
 380 MET   (  71-)  B    5.97
 482 VAL   ( 173-)  B    5.94
 103 PRO   ( 110-)  A    5.87
 168 LEU   ( 175-)  A    5.78
  32 LEU   (  33-)  A    5.72
 745 GLU   ( 120-)  C    5.71
 772 GLY   ( 147-)  C    5.47
 417 ARG   ( 108-)  B    5.44
 566 GLU   ( 257-)  B    5.32
1085 LEU   ( 150-)  D    5.28
 408 ARG   (  99-)  B    5.27
 102 LEU   ( 109-)  A    5.22
 780 THR   ( 155-)  C    5.19
1093 ALA   ( 158-)  D    5.08
1030 ASN   (  95-)  D    5.04
 848 ASP   ( 223-)  C    4.89
 534 GLN   ( 225-)  B    4.79
And so on for a total of 56 lines.

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 : 1.966

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 : -4.801

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.

 817 THR   ( 192-)  C    -3.6
 185 THR   ( 192-)  A    -3.6
 501 THR   ( 192-)  B    -3.5
 709 THR   (  84-)  C    -3.3
  83 THR   (  84-)  A    -3.2
   8 PRO   (   9-)  A    -3.0
 419 PRO   ( 110-)  B    -2.9
 160 HIS   ( 167-)  A    -2.9
 312 LEU   (   3-)  B    -2.8
 448 SER   ( 139-)  B    -2.8
 958 VAL   (  17-)  D    -2.7
1074 SER   ( 139-)  D    -2.7
 744 SER   ( 119-)  C    -2.7
 716 ARG   (  91-)  C    -2.6
1102 HIS   ( 167-)  D    -2.6
 210 SER   ( 217-)  A    -2.6
 399 PRO   (  90-)  B    -2.6
 532 ASP   ( 223-)  B    -2.5
 194 VAL   ( 201-)  A    -2.5
 829 LEU   ( 204-)  C    -2.5
 510 VAL   ( 201-)  B    -2.5
 594 LYS   ( 285-)  B    -2.5
 642 VAL   (  17-)  C    -2.5
 836 VAL   ( 211-)  C    -2.4
 121 LEU   ( 128-)  A    -2.4
And so on for a total of 87 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.

   2 LEU   (   3-)  A  omega poor
   6 ASP   (   7-)  A  Poor phi/psi
   7 TRP   (   8-)  A  PRO omega poor
   9 HIS   (  10-)  A  Poor phi/psi, omega poor
  15 PRO   (  16-)  A  omega poor
  16 VAL   (  17-)  A  omega poor
  21 ASP   (  22-)  A  Poor phi/psi
  24 THR   (  25-)  A  omega poor
  50 HIS   (  51-)  A  omega poor
  56 PRO   (  57-)  A  omega poor
  57 HIS   (  58-)  A  omega poor
  59 THR   (  60-)  A  omega poor
  76 LEU   (  77-)  A  omega poor
  89 LEU   (  96-)  A  Poor phi/psi
  90 ALA   (  97-)  A  omega poor
 114 TYR   ( 121-)  A  Poor phi/psi
 116 GLU   ( 123-)  A  omega poor
 126 GLY   ( 133-)  A  Poor phi/psi, omega poor
 127 ASN   ( 134-)  A  Poor phi/psi, omega poor
 130 GLY   ( 137-)  A  omega poor
 132 SER   ( 139-)  A  omega poor
 133 THR   ( 140-)  A  Poor phi/psi
 138 GLY   ( 145-)  A  omega poor
 143 LEU   ( 150-)  A  omega poor
 160 HIS   ( 167-)  A  Poor phi/psi
And so on for a total of 169 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 : -5.151

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.

 285 SER   ( 292-)  A    0.36
 408 ARG   (  99-)  B    0.36
1151 SER   ( 216-)  D    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 ARG   (   5-)  A      0
   6 ASP   (   7-)  A      0
   7 TRP   (   8-)  A      0
   8 PRO   (   9-)  A      0
   9 HIS   (  10-)  A      0
  10 ALA   (  11-)  A      0
  14 THR   (  15-)  A      0
  16 VAL   (  17-)  A      0
  17 LYS   (  18-)  A      0
  18 ARG   (  19-)  A      0
  20 PHE   (  21-)  A      0
  30 SER   (  31-)  A      0
  50 HIS   (  51-)  A      0
  51 CYS   (  52-)  A      0
  52 SER   (  53-)  A      0
  53 ASP   (  54-)  A      0
  58 ALA   (  59-)  A      0
  82 GLU   (  83-)  A      0
  83 THR   (  84-)  A      0
  85 PRO   (  86-)  A      0
  86 LEU   (  87-)  A      0
  87 GLY   (  94-)  A      0
  88 ASN   (  95-)  A      0
  91 CYS   (  98-)  A      0
 101 ARG   ( 108-)  A      0
And so on for a total of 492 lines.

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 : 9.038

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!

 126 GLY   ( 133-)  A   1.78   80
1068 GLY   ( 133-)  D   1.59   80
 446 GLY   ( 137-)  B   1.53   10

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 844 TRP   ( 219-)  C   1.68

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]

 261 PRO   ( 268-)  A    0.46 HIGH
 536 PRO   ( 227-)  B    0.17 LOW
 622 PRO   ( 313-)  B    0.45 HIGH
1027 PRO   (  86-)  D    0.20 LOW
1045 PRO   ( 110-)  D    0.47 HIGH
1053 PRO   ( 118-)  D    0.13 LOW
1267 PRO   (   4-)  I    0.18 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

   8 PRO   (   9-)  A    -3.6 envelop N (0 degrees)
  85 PRO   (  86-)  A  -135.2 envelop C-delta (-144 degrees)
 111 PRO   ( 118-)  A   112.4 envelop C-beta (108 degrees)
 119 PRO   ( 126-)  A   113.4 envelop C-beta (108 degrees)
 261 PRO   ( 268-)  A  -114.3 envelop C-gamma (-108 degrees)
 271 PRO   ( 278-)  A   -64.4 envelop C-beta (-72 degrees)
 306 PRO   ( 313-)  A   -11.9 half-chair C-alpha/N (-18 degrees)
 318 PRO   (   9-)  B   -56.1 half-chair C-beta/C-alpha (-54 degrees)
 399 PRO   (  90-)  B  -148.0 envelop C-delta (-144 degrees)
 419 PRO   ( 110-)  B   116.5 envelop C-beta (108 degrees)
 475 PRO   ( 166-)  B  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 539 PRO   ( 230-)  B   101.1 envelop C-beta (108 degrees)
 634 PRO   (   9-)  C   -43.4 envelop C-alpha (-36 degrees)
 641 PRO   (  16-)  C  -129.4 half-chair C-delta/C-gamma (-126 degrees)
 710 PRO   (  85-)  C  -124.0 half-chair C-delta/C-gamma (-126 degrees)
 715 PRO   (  90-)  C   -33.5 envelop C-alpha (-36 degrees)
 925 PRO   ( 300-)  C  -132.9 half-chair C-delta/C-gamma (-126 degrees)
1026 PRO   (  85-)  D    45.9 half-chair C-delta/C-gamma (54 degrees)
1248 PRO   ( 313-)  D     3.6 envelop N (0 degrees)
1255 PRO   (   4-)  F    43.4 envelop C-delta (36 degrees)
1259 PRO   (   4-)  G    29.9 envelop C-delta (36 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.

1253 ALA   (   2-)  F      N   <-> 1281 SIN   (   1-)  F      C4     1.23    1.47  INTRA B3
1256 LYS   (   5-)  F      C   <-> 1282 NIT   (   6-)  F      N1     1.22    1.88  INTRA
 986 TYR   (  45-)  D      CE1 <-> 1103 MET   ( 168-)  D      CE     0.70    2.50  INTRA BL
1256 LYS   (   5-)  F      CA  <-> 1282 NIT   (   6-)  F      N1     0.67    2.43  INTRA
 646 PHE   (  21-)  C      N   <->  650 THR   (  25-)  C      CG2    0.64    2.46  INTRA BL
 329 ILE   (  20-)  B      CA  <->  334 THR   (  25-)  B      CG2    0.64    2.56  INTRA BL
1256 LYS   (   5-)  F      O   <-> 1282 NIT   (   6-)  F      N1     0.62    2.08  INTRA
1253 ALA   (   2-)  F      CA  <-> 1281 SIN   (   1-)  F      C4     0.61    2.59  INTRA
 607 LYS   ( 298-)  B      CE  <-> 1271 SIN   (   1-)  H      O3     0.58    2.22  INTRA
 354 TYR   (  45-)  B      CE1 <->  477 MET   ( 168-)  B      CE     0.54    2.66  INTRA BL
 923 LYS   ( 298-)  C      CE  <-> 1269 SIN   (   1-)  G      O3     0.51    2.29  INTRA BL
  88 ASN   (  95-)  A      O   <->   90 ALA   (  97-)  A      N      0.48    2.22  INTRA BL
 538 GLN   ( 229-)  B      O   <->  541 GLU   ( 232-)  B      N      0.45    2.25  INTRA BL
 670 TYR   (  45-)  C      CE1 <->  793 MET   ( 168-)  C      CE     0.45    2.75  INTRA BL
 766 ARG   ( 141-)  C      NH1 <->  768 ASP   ( 143-)  C      OD2    0.45    2.25  INTRA BL
 405 LEU   (  96-)  B      O   <->  407 CYS   (  98-)  B      N      0.44    2.26  INTRA BL
 371 SER   (  62-)  B      OG  <->  373 ILE   (  64-)  B      N      0.43    2.27  INTRA BL
 962 PHE   (  21-)  D      N   <->  966 THR   (  25-)  D      CG2    0.43    2.67  INTRA BL
1253 ALA   (   2-)  F      CA  <-> 1281 SIN   (   1-)  F      O3     0.43    2.37  INTRA
 118 VAL   ( 125-)  A      O   <->  119 PRO   ( 126-)  A      C      0.42    2.18  INTRA BL
1256 LYS   (   5-)  F      C   <-> 1282 NIT   (   6-)  F      C1     0.42    2.78  INTRA
   9 HIS   (  10-)  A      CE1 <-> 1121 ARG   ( 186-)  D      NH1    0.42    2.68  INTRA BL
 478 ARG   ( 169-)  B      NH2 <-> 1278 SO4   (1319-)  D      O1     0.39    2.31  INTRA BL
 468 LEU   ( 159-)  B      CD1 <->  474 PHE   ( 165-)  B      CZ     0.38    2.82  INTRA BL
 679 ASP   (  54-)  C      N   <->  680 PRO   (  55-)  C      CD     0.38    2.62  INTRA BL
And so on for a total of 479 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.

 401 ARG   (  92-)  B      -6.76
 717 ARG   (  92-)  C      -6.39
 569 MET   ( 260-)  B      -6.28
1195 MET   ( 260-)  D      -6.14
 885 MET   ( 260-)  C      -5.93
 575 HIS   ( 266-)  B      -5.89
   4 ARG   (   5-)  A      -5.82
 511 TRP   ( 202-)  B      -5.81
 195 TRP   ( 202-)  A      -5.77
1137 TRP   ( 202-)  D      -5.77
 218 GLN   ( 225-)  A      -5.71
 253 MET   ( 260-)  A      -5.70
 534 GLN   ( 225-)  B      -5.66
 827 TRP   ( 202-)  C      -5.65
 259 HIS   ( 266-)  A      -5.65
 716 ARG   (  91-)  C      -5.65
1201 HIS   ( 266-)  D      -5.63
 891 HIS   ( 266-)  C      -5.61
 319 HIS   (  10-)  B      -5.61
 635 HIS   (  10-)  C      -5.57
 850 GLN   ( 225-)  C      -5.55
1160 GLN   ( 225-)  D      -5.48
 951 HIS   (  10-)  D      -5.38
 683 HIS   (  58-)  C      -5.23
 718 TYR   (  93-)  C      -5.05
 946 ARG   (   5-)  D      -5.02
1024 GLU   (  83-)  D      -5.01

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.

 716 ARG   (  91-)  C       718 - TYR     93- ( C)         -5.69

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

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

1157 LEU   ( 222-)  D   -2.68
 847 LEU   ( 222-)  C   -2.67
 215 LEU   ( 222-)  A   -2.65
 626 ILE   ( 317-)  B   -2.56
1131 ALA   ( 196-)  D   -2.54
 402 TYR   (  93-)  B   -2.54

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.

  67 ASN   (  68-)  A
 115 HIS   ( 122-)  A
 243 GLN   ( 250-)  A
 259 HIS   ( 266-)  A
 309 ASN   ( 316-)  A
 377 ASN   (  68-)  B
 420 GLN   ( 111-)  B
 431 HIS   ( 122-)  B
 516 HIS   ( 207-)  B
 559 GLN   ( 250-)  B
 575 HIS   ( 266-)  B
 747 HIS   ( 122-)  C
 824 HIS   ( 199-)  C
 832 HIS   ( 207-)  C
 875 GLN   ( 250-)  C
 891 HIS   ( 266-)  C
 928 GLN   ( 303-)  C
1009 ASN   (  68-)  D
1057 HIS   ( 122-)  D
1142 HIS   ( 207-)  D
1185 GLN   ( 250-)  D
1201 HIS   ( 266-)  D

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.

   4 ARG   (   5-)  A      N
  12 PHE   (  13-)  A      N
  16 VAL   (  17-)  A      N
  18 ARG   (  19-)  A      N
  18 ARG   (  19-)  A      NE
  19 ILE   (  20-)  A      N
  20 PHE   (  21-)  A      N
  21 ASP   (  22-)  A      N
  36 ARG   (  37-)  A      NE
  63 ILE   (  64-)  A      N
  65 MET   (  66-)  A      N
  89 LEU   (  96-)  A      N
  92 ARG   (  99-)  A      N
  92 ARG   (  99-)  A      NE
 113 GLU   ( 120-)  A      N
 129 PHE   ( 136-)  A      N
 138 GLY   ( 145-)  A      N
 158 PHE   ( 165-)  A      N
 198 ASP   ( 205-)  A      N
 204 VAL   ( 211-)  A      N
 205 TYR   ( 212-)  A      N
 212 TRP   ( 219-)  A      NE1
 214 LEU   ( 221-)  A      N
 221 LEU   ( 228-)  A      N
 237 ASP   ( 244-)  A      N
And so on for a total of 134 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.

  50 HIS   (  51-)  A      ND1
  95 HIS   ( 102-)  A      NE2
 360 HIS   (  51-)  B      ND1
 666 HIS   (  41-)  C      NE2
 676 HIS   (  51-)  C      ND1
 727 HIS   ( 102-)  C      NE2
 768 ASP   ( 143-)  C      OD1
 785 ASP   ( 160-)  C      OD2
 992 HIS   (  51-)  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.

  27 ASP   (  28-)  A   H-bonding suggests Asn
  99 ASP   ( 106-)  A   H-bonding suggests Asn
 120 GLU   ( 127-)  A   H-bonding suggests Gln
 316 ASP   (   7-)  B   H-bonding suggests Asn
 415 ASP   ( 106-)  B   H-bonding suggests Asn; but Alt-Rotamer
 436 GLU   ( 127-)  B   H-bonding suggests Gln; but Alt-Rotamer
 532 ASP   ( 223-)  B   H-bonding suggests Asn
 731 ASP   ( 106-)  C   H-bonding suggests Asn
 848 ASP   ( 223-)  C   H-bonding suggests Asn
 948 ASP   (   7-)  D   H-bonding suggests Asn
 969 ASP   (  28-)  D   H-bonding suggests Asn
1023 ASP   (  82-)  D   H-bonding suggests Asn
1062 GLU   ( 127-)  D   H-bonding suggests Gln; but Alt-Rotamer
1129 GLU   ( 194-)  D   H-bonding suggests Gln
1158 ASP   ( 223-)  D   H-bonding suggests Asn

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 :  -1.665
  2nd generation packing quality :  -2.544
  Ramachandran plot appearance   :  -4.801 (bad)
  chi-1/chi-2 rotamer normality  :  -5.151 (bad)
  Backbone conformation          :  -1.587

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.030
  Bond angles                    :   1.208
  Omega angle restraints         :   1.643 (loose)
  Side chain planarity           :   0.932
  Improper dihedral distribution :   1.285
  Inside/Outside distribution    :   0.997

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 :  -0.8
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.030
  Bond angles                    :   1.208
  Omega angle restraints         :   1.643 (loose)
  Side chain planarity           :   0.932
  Improper dihedral distribution :   1.285
  Inside/Outside distribution    :   0.997
==============

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).

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