WHAT IF Check report

This file was created 2012-01-04 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 pdb1kv3.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 : 0.224
CA-only RMS fit for the two chains : 0.051

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 : 0.334
CA-only RMS fit for the two chains : 0.049

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 : 0.312
CA-only RMS fit for the two chains : 0.055

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: A and E

All-atom RMS fit for the two chains : 0.257
CA-only RMS fit for the two chains : 0.047

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 F

All-atom RMS fit for the two chains : 0.081
CA-only RMS fit for the two chains : 0.039

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.

3913 GDP   ( 700-)  A  -
3914 GDP   ( 701-)  B  -
3915 GDP   ( 702-)  C  -
3916 GDP   ( 703-)  D  -
3917 GDP   ( 704-)  E  -
3918 GDP   ( 705-)  F  -

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

1629 GLU   ( 363-)  C
2319 VAL   ( 402-)  D

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 GLU   (  15-)  A    High
   5 ARG   (  19-)  A    High
  14 ARG   (  28-)  A    High
  15 GLU   (  29-)  A    High
  16 LYS   (  30-)  A    High
  26 TRP   (  40-)  A    High
  27 LEU   (  41-)  A    High
  28 THR   (  42-)  A    High
  29 LEU   (  43-)  A    High
  30 SER   (  56-)  A    High
  31 LEU   (  57-)  A    High
  32 THR   (  58-)  A    High
  34 SER   (  60-)  A    High
  43 GLN   (  69-)  A    High
  44 GLU   (  70-)  A    High
  48 LYS   (  74-)  A    High
  50 ARG   (  76-)  A    High
  52 PRO   (  78-)  A    High
  53 LEU   (  79-)  A    High
  54 ARG   (  80-)  A    High
  55 ASP   (  81-)  A    High
  56 ALA   (  82-)  A    High
  57 VAL   (  83-)  A    High
  58 GLU   (  84-)  A    High
  59 GLU   (  85-)  A    High
And so on for a total of 440 lines.

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:

Crystal temperature (K) :100.000

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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

  89 TYR   ( 115-)  A
 265 TYR   ( 301-)  A
 279 TYR   ( 315-)  A
 352 TYR   ( 388-)  A
 467 TYR   ( 503-)  A
 480 TYR   ( 516-)  A
 492 TYR   ( 528-)  A
 740 TYR   ( 115-)  B
 783 TYR   ( 168-)  B
 930 TYR   ( 315-)  B
1003 TYR   ( 388-)  B
1118 TYR   ( 503-)  B
1131 TYR   ( 516-)  B
1143 TYR   ( 528-)  B
1391 TYR   ( 115-)  C
1567 TYR   ( 301-)  C
1581 TYR   ( 315-)  C
1654 TYR   ( 388-)  C
1769 TYR   ( 503-)  C
1782 TYR   ( 516-)  C
2042 TYR   ( 115-)  D
2232 TYR   ( 315-)  D
2305 TYR   ( 388-)  D
2420 TYR   ( 503-)  D
2433 TYR   ( 516-)  D
2869 TYR   ( 301-)  E
2883 TYR   ( 315-)  E
2956 TYR   ( 388-)  E
3071 TYR   ( 503-)  E
3084 TYR   ( 516-)  E
3096 TYR   ( 528-)  E
3344 TYR   ( 115-)  F
3520 TYR   ( 301-)  F
3534 TYR   ( 315-)  F
3607 TYR   ( 388-)  F
3722 TYR   ( 503-)  F
3735 TYR   ( 516-)  F
3747 TYR   ( 528-)  F

Warning: Phenylalanine convention problem

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

  33 PHE   (  59-)  A
  51 PHE   (  77-)  A
  99 PHE   ( 135-)  A
 130 PHE   ( 166-)  A
 420 PHE   ( 456-)  A
 453 PHE   ( 489-)  A
 501 PHE   ( 537-)  A
 643 PHE   ( 679-)  A
 684 PHE   (  59-)  B
 702 PHE   (  77-)  B
 750 PHE   ( 135-)  B
 781 PHE   ( 166-)  B
1071 PHE   ( 456-)  B
1104 PHE   ( 489-)  B
1152 PHE   ( 537-)  B
1294 PHE   ( 679-)  B
1335 PHE   (  59-)  C
1353 PHE   (  77-)  C
1405 PHE   ( 139-)  C
1432 PHE   ( 166-)  C
1722 PHE   ( 456-)  C
1755 PHE   ( 489-)  C
1803 PHE   ( 537-)  C
1945 PHE   ( 679-)  C
1986 PHE   (  59-)  D
2004 PHE   (  77-)  D
2056 PHE   ( 139-)  D
2083 PHE   ( 166-)  D
2309 PHE   ( 392-)  D
2373 PHE   ( 456-)  D
2406 PHE   ( 489-)  D
2454 PHE   ( 537-)  D
2596 PHE   ( 679-)  D
2637 PHE   (  59-)  E
2655 PHE   (  77-)  E
2734 PHE   ( 166-)  E
3024 PHE   ( 456-)  E
3057 PHE   ( 489-)  E
3105 PHE   ( 537-)  E
3247 PHE   ( 679-)  E
3288 PHE   (  59-)  F
3306 PHE   (  77-)  F
3354 PHE   ( 135-)  F
3385 PHE   ( 166-)  F
3611 PHE   ( 392-)  F
3675 PHE   ( 456-)  F
3708 PHE   ( 489-)  F
3756 PHE   ( 537-)  F
3898 PHE   ( 679-)  F

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.

  11 ASP   (  25-)  A
 155 ASP   ( 191-)  A
 174 ASP   ( 210-)  A
 196 ASP   ( 232-)  A
 206 ASP   ( 242-)  A
 223 ASP   ( 259-)  A
 364 ASP   ( 400-)  A
 373 ASP   ( 409-)  A
 545 ASP   ( 581-)  A
 635 ASP   ( 671-)  A
 662 ASP   (  25-)  B
 806 ASP   ( 191-)  B
 825 ASP   ( 210-)  B
 847 ASP   ( 232-)  B
 857 ASP   ( 242-)  B
 874 ASP   ( 259-)  B
1015 ASP   ( 400-)  B
1024 ASP   ( 409-)  B
1196 ASP   ( 581-)  B
1286 ASP   ( 671-)  B
1313 ASP   (  25-)  C
1457 ASP   ( 191-)  C
1476 ASP   ( 210-)  C
1498 ASP   ( 232-)  C
1508 ASP   ( 242-)  C
And so on for a total of 60 lines.

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.

   1 GLU   (  15-)  A
  44 GLU   (  70-)  A
  58 GLU   (  84-)  A
 119 GLU   ( 155-)  A
 283 GLU   ( 319-)  A
 286 GLU   ( 322-)  A
 316 GLU   ( 352-)  A
 330 GLU   ( 366-)  A
 415 GLU   ( 451-)  A
 466 GLU   ( 502-)  A
 521 GLU   ( 557-)  A
 549 GLU   ( 585-)  A
 611 GLU   ( 647-)  A
 633 GLU   ( 669-)  A
 652 GLU   (  15-)  B
 695 GLU   (  70-)  B
 709 GLU   (  84-)  B
 770 GLU   ( 155-)  B
 934 GLU   ( 319-)  B
 937 GLU   ( 322-)  B
 967 GLU   ( 352-)  B
1066 GLU   ( 451-)  B
1116 GLU   ( 501-)  B
1117 GLU   ( 502-)  B
1172 GLU   ( 557-)  B
And so on for a total of 83 lines.

Geometric checks

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.

 196 ASP   ( 232-)  A      N    CA   C   125.17    5.0
 271 GLN   ( 307-)  A      N    CA   C    93.31   -6.4
 388 LEU   ( 424-)  A      N    CA   C   125.80    5.2
 389 LYS   ( 425-)  A     -C    N    CA  112.88   -4.9
 455 VAL   ( 491-)  A      N    CA   C    98.79   -4.4
 455 VAL   ( 491-)  A      N    CA   CB  117.35    4.0
 457 ALA   ( 493-)  A      N    CA   C    97.86   -4.8
 478 VAL   ( 514-)  A      C    CA   CB   99.86   -5.4
 544 ARG   ( 580-)  A      CB   CG   CD  105.98   -4.1
 766 ASP   ( 151-)  B      N    CA   CB  103.67   -4.0
 847 ASP   ( 232-)  B      N    CA   C   125.07    5.0
 922 GLN   ( 307-)  B      N    CA   C    94.07   -6.1
1039 LEU   ( 424-)  B      N    CA   C   126.00    5.3
1040 LYS   ( 425-)  B     -C    N    CA  112.29   -5.2
1108 ALA   ( 493-)  B      N    CA   C    98.31   -4.6
1129 VAL   ( 514-)  B      C    CA   CB   99.18   -5.7
1498 ASP   ( 232-)  C      N    CA   C   125.08    5.0
1533 HIS   ( 267-)  C      CG   ND1  CE1 109.62    4.0
1573 GLN   ( 307-)  C      N    CA   C    94.09   -6.1
1690 LEU   ( 424-)  C      N    CA   C   126.84    5.6
1691 LYS   ( 425-)  C     -C    N    CA  113.30   -4.7
1707 HIS   ( 441-)  C      CG   ND1  CE1 110.00    4.4
1759 ALA   ( 493-)  C      N    CA   C    99.08   -4.3
1780 VAL   ( 514-)  C      C    CA   CB   99.58   -5.5
2149 ASP   ( 232-)  D      N    CA   C   125.19    5.0
2224 GLN   ( 307-)  D      N    CA   C    94.64   -5.9
2341 LEU   ( 424-)  D      N    CA   C   127.31    5.8
2342 LYS   ( 425-)  D     -C    N    CA  112.83   -4.9
2358 HIS   ( 441-)  D      CG   ND1  CE1 109.68    4.1
2408 VAL   ( 491-)  D      N    CA   C    99.96   -4.0
2410 ALA   ( 493-)  D      N    CA   C    99.32   -4.2
2431 VAL   ( 514-)  D      C    CA   CB  100.19   -5.2
2735 ILE   ( 167-)  E      N    CA   C    99.57   -4.2
2800 ASP   ( 232-)  E      N    CA   C   125.43    5.1
2875 GLN   ( 307-)  E      N    CA   C    94.05   -6.1
2965 VAL   ( 397-)  E      N    CA   CB  103.50   -4.1
2992 LEU   ( 424-)  E      N    CA   C   126.43    5.4
2993 LYS   ( 425-)  E     -C    N    CA  112.54   -5.1
3061 ALA   ( 493-)  E      N    CA   C    97.84   -4.8
3082 VAL   ( 514-)  E      C    CA   CB  100.22   -5.2
3386 ILE   ( 167-)  F      C    CA   CB  102.43   -4.0
3451 ASP   ( 232-)  F      N    CA   C   125.21    5.0
3526 GLN   ( 307-)  F      N    CA   C    93.22   -6.4
3616 VAL   ( 397-)  F      N    CA   CB  103.60   -4.1
3643 LEU   ( 424-)  F      N    CA   C   125.75    5.2
3644 LYS   ( 425-)  F     -C    N    CA  112.93   -4.9
3712 ALA   ( 493-)  F      N    CA   C    98.01   -4.7
3733 VAL   ( 514-)  F      C    CA   CB  101.33   -4.6

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.

   1 GLU   (  15-)  A
  11 ASP   (  25-)  A
  44 GLU   (  70-)  A
  58 GLU   (  84-)  A
 119 GLU   ( 155-)  A
 155 ASP   ( 191-)  A
 174 ASP   ( 210-)  A
 196 ASP   ( 232-)  A
 206 ASP   ( 242-)  A
 223 ASP   ( 259-)  A
 283 GLU   ( 319-)  A
 286 GLU   ( 322-)  A
 316 GLU   ( 352-)  A
 330 GLU   ( 366-)  A
 364 ASP   ( 400-)  A
 373 ASP   ( 409-)  A
 415 GLU   ( 451-)  A
 466 GLU   ( 502-)  A
 521 GLU   ( 557-)  A
 545 ASP   ( 581-)  A
 549 GLU   ( 585-)  A
 611 GLU   ( 647-)  A
 633 GLU   ( 669-)  A
 635 ASP   ( 671-)  A
 652 GLU   (  15-)  B
And so on for a total of 143 lines.

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.

3526 GLN   ( 307-)  F    7.13
 271 GLN   ( 307-)  A    7.10
2875 GLN   ( 307-)  E    6.80
 922 GLN   ( 307-)  B    6.79
1573 GLN   ( 307-)  C    6.79
2224 GLN   ( 307-)  D    6.57
2341 LEU   ( 424-)  D    6.50
1690 LEU   ( 424-)  C    6.31
2992 LEU   ( 424-)  E    6.15
1039 LEU   ( 424-)  B    5.97
 388 LEU   ( 424-)  A    5.89
3643 LEU   ( 424-)  F    5.87
 892 CYS   ( 277-)  B    5.42
2845 CYS   ( 277-)  E    5.19
1543 CYS   ( 277-)  C    5.06
3061 ALA   ( 493-)  E    4.94
 457 ALA   ( 493-)  A    4.93
2194 CYS   ( 277-)  D    4.91
3712 ALA   ( 493-)  F    4.87
 361 VAL   ( 397-)  A    4.80
2800 ASP   ( 232-)  E    4.79
3496 CYS   ( 277-)  F    4.78
1108 ALA   ( 493-)  B    4.74
3451 ASP   ( 232-)  F    4.72
2149 ASP   ( 232-)  D    4.71
And so on for a total of 51 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 : 1.531

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.

2085 TYR   ( 168-)  D      CB   4.38
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.228

Torsion-related checks

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.

  39 PRO   (  65-)  A    -2.9
1341 PRO   (  65-)  C    -2.9
1992 PRO   (  65-)  D    -2.9
2643 PRO   (  65-)  E    -2.9
3294 PRO   (  65-)  F    -2.9
 690 PRO   (  65-)  B    -2.9
1896 THR   ( 630-)  C    -2.7
 637 LEU   ( 673-)  A    -2.6
3849 THR   ( 630-)  F    -2.6
3241 LEU   ( 673-)  E    -2.6
3892 LEU   ( 673-)  F    -2.6
1288 LEU   ( 673-)  B    -2.6
1939 LEU   ( 673-)  C    -2.6
3198 THR   ( 630-)  E    -2.6
3312 VAL   (  83-)  F    -2.6
 708 VAL   (  83-)  B    -2.6
1359 VAL   (  83-)  C    -2.6
  57 VAL   (  83-)  A    -2.6
2010 VAL   (  83-)  D    -2.6
2590 LEU   ( 673-)  D    -2.6
2661 VAL   (  83-)  E    -2.6
 594 THR   ( 630-)  A    -2.6
2547 THR   ( 630-)  D    -2.6
1245 THR   ( 630-)  B    -2.5
1093 ARG   ( 478-)  B    -2.5
And so on for a total of 187 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.

   8 HIS   (  22-)  A  Poor phi/psi
  15 GLU   (  29-)  A  Poor phi/psi
  16 LYS   (  30-)  A  Poor phi/psi
  55 ASP   (  81-)  A  Poor phi/psi
  56 ALA   (  82-)  A  Poor phi/psi
  57 VAL   (  83-)  A  Poor phi/psi
  58 GLU   (  84-)  A  Poor phi/psi
  59 GLU   (  85-)  A  Poor phi/psi
  61 ASP   (  87-)  A  Poor phi/psi
  70 GLN   (  96-)  A  Poor phi/psi
  71 ASP   (  97-)  A  Poor phi/psi
  95 ALA   ( 121-)  A  Poor phi/psi
 133 GLN   ( 169-)  A  Poor phi/psi
 147 GLY   ( 183-)  A  Poor phi/psi
 193 ASN   ( 229-)  A  Poor phi/psi
 194 CYS   ( 230-)  A  Poor phi/psi
 195 ASN   ( 231-)  A  Poor phi/psi
 207 ASN   ( 243-)  A  Poor phi/psi
 233 CYS   ( 269-)  A  Poor phi/psi
 237 LYS   ( 273-)  A  omega poor
 266 ASN   ( 302-)  A  Poor phi/psi
 270 ASP   ( 306-)  A  Poor phi/psi
 272 ASN   ( 308-)  A  Poor phi/psi
 273 SER   ( 309-)  A  Poor phi/psi
 289 GLY   ( 325-)  A  Poor phi/psi
And so on for a total of 228 lines.

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 : -3.456

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.

 189 SER   ( 225-)  A    0.35
3444 SER   ( 225-)  F    0.35
2142 SER   ( 225-)  D    0.36
2793 SER   ( 225-)  E    0.36
1491 SER   ( 225-)  C    0.37
 341 ARG   ( 377-)  A    0.38
 840 SER   ( 225-)  B    0.38

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!

   8 HIS   (  22-)  A      0
   9 THR   (  23-)  A      0
  13 CYS   (  27-)  A      0
  14 ARG   (  28-)  A      0
  15 GLU   (  29-)  A      0
  21 ARG   (  35-)  A      0
  28 THR   (  42-)  A      0
  29 LEU   (  43-)  A      0
  30 SER   (  56-)  A      0
  31 LEU   (  57-)  A      0
  40 ALA   (  66-)  A      0
  41 PRO   (  67-)  A      0
  43 GLN   (  69-)  A      0
  45 ALA   (  71-)  A      0
  47 THR   (  73-)  A      0
  53 LEU   (  79-)  A      0
  55 ASP   (  81-)  A      0
  56 ALA   (  82-)  A      0
  57 VAL   (  83-)  A      0
  58 GLU   (  84-)  A      0
  59 GLU   (  85-)  A      0
  61 ASP   (  87-)  A      0
  62 TRP   (  88-)  A      0
  64 ALA   (  90-)  A      0
  67 VAL   (  93-)  A      0
And so on for a total of 1715 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 : 1.762

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!

3194 GLY   ( 626-)  E   1.70   14
1241 GLY   ( 626-)  B   1.68   18
3845 GLY   ( 626-)  F   1.65   13
 590 GLY   ( 626-)  A   1.62   14
1892 GLY   ( 626-)  C   1.60   15
2991 GLY   ( 423-)  E   1.58   25
2543 GLY   ( 626-)  D   1.56   14
3642 GLY   ( 423-)  F   1.53   23
 387 GLY   ( 423-)  A   1.53   25
 609 GLY   ( 645-)  A   1.52   52

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...

  70 GLN   (  96-)  A   1.57
1372 GLN   (  96-)  C   1.58
2023 GLN   (  96-)  D   1.91
2674 GLN   (  96-)  E   1.53
3325 GLN   (  96-)  F   1.76
3862 GLU   ( 643-)  F   1.52

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]

 675 PRO   (  38-)  B    0.46 HIGH
 988 PRO   ( 373-)  B    0.46 HIGH
1227 PRO   ( 612-)  B    0.47 HIGH
1326 PRO   (  38-)  C    0.45 HIGH
1952 PRO   ( 686-)  C    0.45 HIGH
2290 PRO   ( 373-)  D    0.46 HIGH
2941 PRO   ( 373-)  E    0.45 HIGH
3138 PRO   ( 570-)  E    0.46 HIGH
3180 PRO   ( 612-)  E    0.46 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].

  85 PRO   ( 111-)  A  -114.3 envelop C-gamma (-108 degrees)
 692 PRO   (  67-)  B  -112.5 envelop C-gamma (-108 degrees)
 736 PRO   ( 111-)  B  -112.3 envelop C-gamma (-108 degrees)
1256 PRO   ( 641-)  B  -112.6 envelop C-gamma (-108 degrees)
1387 PRO   ( 111-)  C  -112.0 envelop C-gamma (-108 degrees)
2038 PRO   ( 111-)  D  -114.9 envelop C-gamma (-108 degrees)
3340 PRO   ( 111-)  F  -113.5 envelop C-gamma (-108 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.

1846 ARG   ( 580-)  C      NH1 <-> 3921 HOH   ( 751 )  C      O      0.43    2.27  INTRA BL
1160 CYS   ( 545-)  B      SG  <-> 3920 HOH   ( 723 )  B      O      0.38    2.62  INTRA BL
2395 ARG   ( 478-)  D      NH2 <-> 3046 ARG   ( 478-)  E      NH2    0.37    2.48  INTRA BF
2845 CYS   ( 277-)  E      SG  <-> 3084 TYR   ( 516-)  E      OH     0.36    2.64  INTRA BL
1543 CYS   ( 277-)  C      SG  <-> 1782 TYR   ( 516-)  C      OH     0.33    2.67  INTRA BL
3596 ARG   ( 377-)  F      N   <-> 3924 HOH   ( 727 )  F      O      0.33    2.37  INTRA BL
1371 GLN   (  95-)  C      O   <-> 1373 ASP   (  97-)  C      N      0.32    2.38  INTRA BF
2673 GLN   (  95-)  E      O   <-> 2675 ASP   (  97-)  E      N      0.32    2.38  INTRA BF
2022 GLN   (  95-)  D      O   <-> 2024 ASP   (  97-)  D      N      0.31    2.39  INTRA BF
3496 CYS   ( 277-)  F      SG  <-> 3735 TYR   ( 516-)  F      OH     0.31    2.69  INTRA BL
3552 ASN   ( 333-)  F      ND2 <-> 3800 ASP   ( 581-)  F      CG     0.30    2.80  INTRA BL
1588 GLU   ( 322-)  C      OE1 <-> 1778 ARG   ( 512-)  C      NH1    0.29    2.41  INTRA BF
1599 ASN   ( 333-)  C      ND2 <-> 1847 ASP   ( 581-)  C      CG     0.29    2.81  INTRA BL
3078 CYS   ( 510-)  E      SG  <-> 3091 GLU   ( 523-)  E      CG     0.29    3.11  INTRA BF
2875 GLN   ( 307-)  E      O   <-> 2877 SER   ( 309-)  E      N      0.28    2.42  INTRA BF
 941 ASP   ( 326-)  B      CG  <->  942 LYS   ( 327-)  B      N      0.27    2.73  INTRA BF
1852 ASN   ( 586-)  C      N   <-> 3921 HOH   ( 729 )  C      O      0.27    2.43  INTRA BL
 470 ARG   ( 506-)  A      NH1 <-> 2445 TYR   ( 528-)  D      OH     0.27    2.43  INTRA BL
 431 GLU   ( 467-)  A      O   <->  433 GLU   ( 469-)  A      N      0.27    2.43  INTRA BF
3324 GLN   (  95-)  F      O   <-> 3326 ASP   (  97-)  F      N      0.27    2.43  INTRA BF
2781 ARG   ( 213-)  E      O   <-> 2783 SER   ( 215-)  E      N      0.27    2.43  INTRA BF
2481 ARG   ( 564-)  D      NE  <-> 3922 HOH   ( 711 )  D      O      0.26    2.44  INTRA BL
3035 GLU   ( 467-)  E      O   <-> 3037 GLU   ( 469-)  E      N      0.26    2.44  INTRA BF
2224 GLN   ( 307-)  D      O   <-> 2226 SER   ( 309-)  D      N      0.26    2.44  INTRA BF
 948 ASN   ( 333-)  B      ND2 <-> 1196 ASP   ( 581-)  B      CG     0.26    2.84  INTRA BL
And so on for a total of 452 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

2916 GLN   ( 348-)  E      -6.91
3567 GLN   ( 348-)  F      -6.90
 963 GLN   ( 348-)  B      -6.90
2265 GLN   ( 348-)  D      -6.87
1614 GLN   ( 348-)  C      -6.86
 312 GLN   ( 348-)  A      -6.84
2305 TYR   ( 388-)  D      -6.42
2956 TYR   ( 388-)  E      -6.40
 352 TYR   ( 388-)  A      -6.40
3607 TYR   ( 388-)  F      -6.34
1003 TYR   ( 388-)  B      -6.26
1654 TYR   ( 388-)  C      -6.25
1080 LEU   ( 465-)  B      -6.06
2382 LEU   ( 465-)  D      -6.04
3684 LEU   ( 465-)  F      -6.03
3033 LEU   ( 465-)  E      -6.03
1731 LEU   ( 465-)  C      -6.01
 429 LEU   ( 465-)  A      -6.01
1316 ARG   (  28-)  C      -6.00
3269 ARG   (  28-)  F      -5.99
2618 ARG   (  28-)  E      -5.99
 665 ARG   (  28-)  B      -5.98
  14 ARG   (  28-)  A      -5.98
1967 ARG   (  28-)  D      -5.90
3262 HIS   (  21-)  F      -5.71
And so on for a total of 98 lines.

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.

  57 VAL   (  83-)  A        59 - GLU     85- ( A)         -4.66
 621 LEU   ( 657-)  A       623 - MET    659- ( A)         -4.86
 708 VAL   (  83-)  B       710 - GLU     85- ( B)         -4.65
1215 LYS   ( 600-)  B      1217 - LYS    602- ( B)         -4.65
1272 LEU   ( 657-)  B      1274 - MET    659- ( B)         -4.85
1359 VAL   (  83-)  C      1361 - GLU     85- ( C)         -4.65
1866 LYS   ( 600-)  C      1868 - LYS    602- ( C)         -4.62
1923 LEU   ( 657-)  C      1925 - MET    659- ( C)         -4.85
2010 VAL   (  83-)  D      2012 - GLU     85- ( D)         -4.67
2517 LYS   ( 600-)  D      2519 - LYS    602- ( D)         -4.66
2574 LEU   ( 657-)  D      2576 - MET    659- ( D)         -4.87
2661 VAL   (  83-)  E      2663 - GLU     85- ( E)         -4.66
3168 LYS   ( 600-)  E      3170 - LYS    602- ( E)         -4.58
3225 LEU   ( 657-)  E      3227 - MET    659- ( E)         -4.86
3312 VAL   (  83-)  F      3314 - GLU     85- ( F)         -4.63
3876 LEU   ( 657-)  F      3878 - MET    659- ( F)         -4.88

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: 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: E

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: F

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.

3736 ASN   ( 517-)  F   -2.88
 481 ASN   ( 517-)  A   -2.86
3085 ASN   ( 517-)  E   -2.83
2434 ASN   ( 517-)  D   -2.82
1132 ASN   ( 517-)  B   -2.80
1783 ASN   ( 517-)  C   -2.79
1578 LEU   ( 312-)  C   -2.59
3588 TYR   ( 369-)  F   -2.50

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 426 LEU   ( 462-)  A     -  430 ALA   ( 466-)  A        -1.84

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

3919 HOH   ( 713 )  A      O
3919 HOH   ( 715 )  A      O
3919 HOH   ( 730 )  A      O
3919 HOH   ( 731 )  A      O
3919 HOH   ( 764 )  A      O
3920 HOH   ( 738 )  B      O
3920 HOH   ( 759 )  B      O
3920 HOH   ( 765 )  B      O
3920 HOH   ( 768 )  B      O
3921 HOH   ( 715 )  C      O
3921 HOH   ( 717 )  C      O
3921 HOH   ( 723 )  C      O
3921 HOH   ( 736 )  C      O
3921 HOH   ( 740 )  C      O
3921 HOH   ( 755 )  C      O
3921 HOH   ( 779 )  C      O
3921 HOH   ( 798 )  C      O
3922 HOH   ( 716 )  D      O
3922 HOH   ( 728 )  D      O
3922 HOH   ( 767 )  D      O
3923 HOH   ( 719 )  E      O
3923 HOH   ( 733 )  E      O
3923 HOH   ( 765 )  E      O
3924 HOH   ( 723 )  F      O
3924 HOH   ( 726 )  F      O

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.

 170 ASN   ( 206-)  A
 234 GLN   ( 270-)  A
 326 GLN   ( 362-)  A
 821 ASN   ( 206-)  B
 885 GLN   ( 270-)  B
 977 GLN   ( 362-)  B
1273 HIS   ( 658-)  B
1472 ASN   ( 206-)  C
1536 GLN   ( 270-)  C
2123 ASN   ( 206-)  D
2187 GLN   ( 270-)  D
2279 GLN   ( 362-)  D
2575 HIS   ( 658-)  D
2774 ASN   ( 206-)  E
2838 GLN   ( 270-)  E
2930 GLN   ( 362-)  E
3425 ASN   ( 206-)  F
3489 GLN   ( 270-)  F
3581 GLN   ( 362-)  F
3877 HIS   ( 658-)  F

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.

   3 ASN   (  17-)  A      N
  20 ARG   (  34-)  A      NH2
  21 ARG   (  35-)  A      NE
  23 GLN   (  37-)  A      N
  42 SER   (  68-)  A      N
  47 THR   (  73-)  A      N
  70 GLN   (  96-)  A      N
  74 LEU   ( 100-)  A      N
  80 THR   ( 106-)  A      OG1
 105 ALA   ( 141-)  A      N
 116 SER   ( 152-)  A      N
 116 SER   ( 152-)  A      OG
 128 GLN   ( 164-)  A      N
 132 TYR   ( 168-)  A      N
 155 ASP   ( 191-)  A      N
 222 VAL   ( 258-)  A      N
 234 GLN   ( 270-)  A      N
 235 ARG   ( 271-)  A      NE
 240 GLN   ( 276-)  A      N
 265 TYR   ( 301-)  A      N
 271 GLN   ( 307-)  A      N
 274 ASN   ( 310-)  A      N
 291 LYS   ( 327-)  A      N
 297 ASN   ( 333-)  A      ND2
 298 PHE   ( 334-)  A      N
And so on for a total of 287 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.

 128 GLN   ( 164-)  A      OE1
 133 GLN   ( 169-)  A      OE1
 264 ASN   ( 300-)  A      OD1
 269 HIS   ( 305-)  A      NE2
 425 HIS   ( 461-)  A      ND1
 461 ASN   ( 497-)  A      OD1
 622 HIS   ( 658-)  A      ND1
 631 ASN   ( 667-)  A      OD1
 749 HIS   ( 134-)  B      ND1
 779 GLN   ( 164-)  B      OE1
 784 GLN   ( 169-)  B      OE1
 915 ASN   ( 300-)  B      OD1
1076 HIS   ( 461-)  B      ND1
1112 ASN   ( 497-)  B      OD1
1282 ASN   ( 667-)  B      OD1
1400 HIS   ( 134-)  C      ND1
1430 GLN   ( 164-)  C      OE1
1566 ASN   ( 300-)  C      OD1
1727 HIS   ( 461-)  C      ND1
1763 ASN   ( 497-)  C      OD1
1924 HIS   ( 658-)  C      ND1
1933 ASN   ( 667-)  C      OD1
1961 HIS   (  22-)  D      ND1
2051 HIS   ( 134-)  D      ND1
2081 GLN   ( 164-)  D      OE1
2086 GLN   ( 169-)  D      OE1
2217 ASN   ( 300-)  D      OD1
2378 HIS   ( 461-)  D      ND1
2414 ASN   ( 497-)  D      OD1
2584 ASN   ( 667-)  D      OD1
2702 HIS   ( 134-)  E      ND1
2732 GLN   ( 164-)  E      OE1
2737 GLN   ( 169-)  E      OE1
2868 ASN   ( 300-)  E      OD1
2873 HIS   ( 305-)  E      NE2
3065 ASN   ( 497-)  E      OD1
3235 ASN   ( 667-)  E      OD1
3353 HIS   ( 134-)  F      ND1
3383 GLN   ( 164-)  F      OE1
3388 GLN   ( 169-)  F      OE1
3519 ASN   ( 300-)  F      OD1
3716 ASN   ( 497-)  F      OD1
3886 ASN   ( 667-)  F      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

3920 HOH   ( 733 )  B      O  0.89  K  4

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.

   6 ASP   (  20-)  A   H-bonding suggests Asn
  61 ASP   (  87-)  A   H-bonding suggests Asn; but Alt-Rotamer
 290 ASP   ( 326-)  A   H-bonding suggests Asn
 657 ASP   (  20-)  B   H-bonding suggests Asn
 712 ASP   (  87-)  B   H-bonding suggests Asn; but Alt-Rotamer
1286 ASP   ( 671-)  B   H-bonding suggests Asn
1308 ASP   (  20-)  C   H-bonding suggests Asn
1363 ASP   (  87-)  C   H-bonding suggests Asn; but Alt-Rotamer
1592 ASP   ( 326-)  C   H-bonding suggests Asn
1937 ASP   ( 671-)  C   H-bonding suggests Asn
1959 ASP   (  20-)  D   H-bonding suggests Asn
2014 ASP   (  87-)  D   H-bonding suggests Asn; but Alt-Rotamer
2236 GLU   ( 319-)  D   H-bonding suggests Gln
2243 ASP   ( 326-)  D   H-bonding suggests Asn
2588 ASP   ( 671-)  D   H-bonding suggests Asn
2610 ASP   (  20-)  E   H-bonding suggests Asn
2665 ASP   (  87-)  E   H-bonding suggests Asn; but Alt-Rotamer
2894 ASP   ( 326-)  E   H-bonding suggests Asn
3239 ASP   ( 671-)  E   H-bonding suggests Asn
3261 ASP   (  20-)  F   H-bonding suggests Asn
3316 ASP   (  87-)  F   H-bonding suggests Asn; but Alt-Rotamer
3545 ASP   ( 326-)  F   H-bonding suggests Asn
3890 ASP   ( 671-)  F   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 :  -0.760
  2nd generation packing quality :  -2.073
  Ramachandran plot appearance   :  -2.228
  chi-1/chi-2 rotamer normality  :  -3.456 (poor)
  Backbone conformation          :  -0.236

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.561 (tight)
  Bond angles                    :   0.804
  Omega angle restraints         :   0.320 (tight)
  Side chain planarity           :   0.540 (tight)
  Improper dihedral distribution :   1.040
  B-factor distribution          :   1.086
  Inside/Outside distribution    :   1.032

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 :   0.4
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.561 (tight)
  Bond angles                    :   0.804
  Omega angle restraints         :   0.320 (tight)
  Side chain planarity           :   0.540 (tight)
  Improper dihedral distribution :   1.040
  B-factor distribution          :   1.086
  Inside/Outside distribution    :   1.032
==============

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.