WHAT IF Check report

This file was created 2012-01-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1v0e.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 : 0.482
CA-only RMS fit for the two chains : 0.432

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.442
CA-only RMS fit for the two chains : 0.362

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 : 0.302
CA-only RMS fit for the two chains : 0.198

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 : 0.429
CA-only RMS fit for the two chains : 0.377

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 : 0.483
CA-only RMS fit for the two chains : 0.431

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 F

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.

3997 PO4   (1685-)  B  -
3998 PO4   (1685-)  C  -
3999 PO4   (1686-)  C  -
4000 PO4   (1685-)  D  -
4001 PO4   (1685-)  F  -
4002 PO4   (1686-)  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.

2221 VAL   ( 467-)  D
3715 THR   ( 629-)  F

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: Arginine nomenclature problem

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

  44 ARG   ( 288-)  A
 152 ARG   ( 396-)  A
 162 ARG   ( 406-)  A
 269 ARG   ( 513-)  A
 325 ARG   ( 569-)  A
 352 ARG   ( 596-)  A
 355 ARG   ( 599-)  A
 365 ARG   ( 609-)  A
 416 ARG   ( 660-)  A
 428 ARG   ( 672-)  A
 540 ARG   ( 784-)  A
 568 ARG   ( 812-)  A
 710 ARG   ( 288-)  B
 818 ARG   ( 396-)  B
 828 ARG   ( 406-)  B
 935 ARG   ( 513-)  B
 991 ARG   ( 569-)  B
1018 ARG   ( 596-)  B
1021 ARG   ( 599-)  B
1031 ARG   ( 609-)  B
1082 ARG   ( 660-)  B
1094 ARG   ( 672-)  B
1206 ARG   ( 784-)  B
1234 ARG   ( 812-)  B
1376 ARG   ( 288-)  C
And so on for a total of 72 lines.

Warning: Tyrosine convention problem

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

  34 TYR   ( 278-)  A
  52 TYR   ( 296-)  A
  62 TYR   ( 306-)  A
  80 TYR   ( 324-)  A
 100 TYR   ( 344-)  A
 343 TYR   ( 587-)  A
 417 TYR   ( 661-)  A
 421 TYR   ( 665-)  A
 449 TYR   ( 693-)  A
 471 TYR   ( 715-)  A
 485 TYR   ( 729-)  A
 522 TYR   ( 766-)  A
 613 TYR   ( 857-)  A
 625 TYR   ( 869-)  A
 700 TYR   ( 278-)  B
 718 TYR   ( 296-)  B
 728 TYR   ( 306-)  B
 746 TYR   ( 324-)  B
 766 TYR   ( 344-)  B
 988 TYR   ( 566-)  B
1009 TYR   ( 587-)  B
1083 TYR   ( 661-)  B
1087 TYR   ( 665-)  B
1115 TYR   ( 693-)  B
1137 TYR   ( 715-)  B
And so on for a total of 95 lines.

Warning: Phenylalanine convention problem

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

  73 PHE   ( 317-)  A
 156 PHE   ( 400-)  A
 212 PHE   ( 456-)  A
 238 PHE   ( 482-)  A
 263 PHE   ( 507-)  A
 285 PHE   ( 529-)  A
 312 PHE   ( 556-)  A
 378 PHE   ( 622-)  A
 389 PHE   ( 633-)  A
 474 PHE   ( 718-)  A
 520 PHE   ( 764-)  A
 533 PHE   ( 777-)  A
 548 PHE   ( 792-)  A
 579 PHE   ( 823-)  A
 596 PHE   ( 840-)  A
 654 PHE   ( 898-)  A
 739 PHE   ( 317-)  B
 822 PHE   ( 400-)  B
 878 PHE   ( 456-)  B
 881 PHE   ( 459-)  B
 951 PHE   ( 529-)  B
 978 PHE   ( 556-)  B
1044 PHE   ( 622-)  B
1055 PHE   ( 633-)  B
1091 PHE   ( 669-)  B
And so on for a total of 89 lines.

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.

   5 ASP   ( 249-)  A
   9 ASP   ( 253-)  A
  87 ASP   ( 331-)  A
 104 ASP   ( 348-)  A
 120 ASP   ( 364-)  A
 121 ASP   ( 365-)  A
 137 ASP   ( 381-)  A
 204 ASP   ( 448-)  A
 211 ASP   ( 455-)  A
 234 ASP   ( 478-)  A
 289 ASP   ( 533-)  A
 301 ASP   ( 545-)  A
 314 ASP   ( 558-)  A
 334 ASP   ( 578-)  A
 368 ASP   ( 612-)  A
 395 ASP   ( 639-)  A
 438 ASP   ( 682-)  A
 478 ASP   ( 722-)  A
 502 ASP   ( 746-)  A
 513 ASP   ( 757-)  A
 551 ASP   ( 795-)  A
 671 ASP   ( 249-)  B
 675 ASP   ( 253-)  B
 753 ASP   ( 331-)  B
 770 ASP   ( 348-)  B
And so on for a total of 128 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.

  65 GLU   ( 309-)  A
  66 GLU   ( 310-)  A
  71 GLU   ( 315-)  A
 281 GLU   ( 525-)  A
 306 GLU   ( 550-)  A
 330 GLU   ( 574-)  A
 332 GLU   ( 576-)  A
 374 GLU   ( 618-)  A
 409 GLU   ( 653-)  A
 440 GLU   ( 684-)  A
 570 GLU   ( 814-)  A
 574 GLU   ( 818-)  A
 576 GLU   ( 820-)  A
 600 GLU   ( 844-)  A
 629 GLU   ( 873-)  A
 732 GLU   ( 310-)  B
 737 GLU   ( 315-)  B
 947 GLU   ( 525-)  B
 972 GLU   ( 550-)  B
 998 GLU   ( 576-)  B
1040 GLU   ( 618-)  B
1075 GLU   ( 653-)  B
1106 GLU   ( 684-)  B
1236 GLU   ( 814-)  B
1240 GLU   ( 818-)  B
And so on for a total of 85 lines.

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.

 458 VAL   ( 702-)  A      CA   CB    1.62    4.7

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.511
RMS-deviation in bond distances: 0.013

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

 |  0.996731 -0.000093 -0.000042|
 | -0.000093  0.997604 -0.000079|
 | -0.000042 -0.000079  0.997207|
Proposed new scale matrix

 |  0.010068  0.000000  0.000000|
 |  0.000000  0.007637  0.000000|
 |  0.000000  0.000000  0.002892|
With corresponding cell

    A    =  99.325  B   = 130.936  C    = 345.772
    Alpha=  90.003  Beta=  90.003  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  99.650  B   = 131.250  C    = 346.700
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1083.694
(Under-)estimated Z-score: 24.262

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.

  51 VAL   ( 295-)  A      N    CA   CB  117.82    4.3
  51 VAL   ( 295-)  A      C    CA   CB   98.30   -6.2
 111 LEU   ( 355-)  A      CA   CB   CG  135.02    5.3
 260 GLY   ( 504-)  A     -CA  -C    N   125.12    4.5
 260 GLY   ( 504-)  A     -C    N    CA  129.30    5.1
 352 ARG   ( 596-)  A      CD   NE   CZ  129.10    4.1
 376 LEU   ( 620-)  A      CA   CB   CG  130.40    4.0
 383 HIS   ( 627-)  A      CG   ND1  CE1 109.77    4.2
 630 HIS   ( 874-)  A      CG   ND1  CE1 109.65    4.1
 717 VAL   ( 295-)  B      C    CA   CB  100.60   -5.0
 777 LEU   ( 355-)  B      CA   CB   CG  131.29    4.3
1042 LEU   ( 620-)  B      CA   CB   CG  134.52    5.2
1383 VAL   ( 295-)  C      C    CA   CB  101.12   -4.7
1443 LEU   ( 355-)  C      CA   CB   CG  134.93    5.3
1456 THR   ( 368-)  C      N    CA   CB  102.80   -4.5
1564 VAL   ( 476-)  C      C    CA   CB  117.95    4.1
1592 GLY   ( 504-)  C     -O   -C    N   116.07   -4.3
1592 GLY   ( 504-)  C     -CA  -C    N   126.04    4.9
1592 GLY   ( 504-)  C     -C    N    CA  130.03    5.5
1708 LEU   ( 620-)  C      CA   CB   CG  131.74    4.4
2049 VAL   ( 295-)  D      C    CA   CB  101.25   -4.7
2109 LEU   ( 355-)  D      CA   CB   CG  135.26    5.4
2258 GLY   ( 504-)  D     -C    N    CA  128.83    4.8
2259 THR   ( 505-)  D     -CA  -C    N   125.99    4.6
2374 LEU   ( 620-)  D      CA   CB   CG  134.49    5.2
2715 VAL   ( 295-)  E      C    CA   CB  101.26   -4.7
2775 LEU   ( 355-)  E      CA   CB   CG  134.67    5.2
2788 THR   ( 368-)  E      N    CA   CB  103.31   -4.2
3381 VAL   ( 295-)  F      C    CA   CB  100.93   -4.8
3441 LEU   ( 355-)  F      CA   CB   CG  134.25    5.1
3590 GLY   ( 504-)  F     -CA  -C    N   125.42    4.6
3590 GLY   ( 504-)  F     -C    N    CA  128.56    4.7
3591 THR   ( 505-)  F     -CA  -C    N   124.90    4.0
3706 LEU   ( 620-)  F      CA   CB   CG  131.89    4.5
3851 ARG   ( 765-)  F      CG   CD   NE  118.76    4.9

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.

   5 ASP   ( 249-)  A
   9 ASP   ( 253-)  A
  44 ARG   ( 288-)  A
  65 GLU   ( 309-)  A
  66 GLU   ( 310-)  A
  71 GLU   ( 315-)  A
  87 ASP   ( 331-)  A
 104 ASP   ( 348-)  A
 120 ASP   ( 364-)  A
 121 ASP   ( 365-)  A
 137 ASP   ( 381-)  A
 152 ARG   ( 396-)  A
 162 ARG   ( 406-)  A
 204 ASP   ( 448-)  A
 211 ASP   ( 455-)  A
 234 ASP   ( 478-)  A
 269 ARG   ( 513-)  A
 281 GLU   ( 525-)  A
 289 ASP   ( 533-)  A
 301 ASP   ( 545-)  A
 306 GLU   ( 550-)  A
 314 ASP   ( 558-)  A
 325 ARG   ( 569-)  A
 330 GLU   ( 574-)  A
 332 GLU   ( 576-)  A
And so on for a total of 285 lines.

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.

  51 VAL   ( 295-)  A      CB     9.2   -20.88   -32.96
 458 VAL   ( 702-)  A      CB     6.5   -24.39   -32.96
 717 VAL   ( 295-)  B      CB     6.1   -25.00   -32.96
 757 VAL   ( 335-)  B      CB     6.6   -24.27   -32.96
1124 VAL   ( 702-)  B      CA    -6.3    24.10    33.23
1124 VAL   ( 702-)  B      CB     6.9   -23.86   -32.96
1176 ILE   ( 754-)  B      CB    -8.1    21.73    32.31
1790 VAL   ( 702-)  C      CB     6.6   -24.27   -32.96
1842 ILE   ( 754-)  C      CB    -6.0    24.45    32.31
2049 VAL   ( 295-)  D      CB     6.4   -24.54   -32.96
2456 VAL   ( 702-)  D      CB     6.0   -25.08   -32.96
3122 VAL   ( 702-)  E      CA    -7.0    23.12    33.23
3122 VAL   ( 702-)  E      CB     7.5   -23.19   -32.96
3421 VAL   ( 335-)  F      CB     6.2   -24.79   -32.96
3788 VAL   ( 702-)  F      CA    -6.7    23.59    33.23
3840 ILE   ( 754-)  F      CB    -8.3    21.53    32.31
The average deviation= 0.986

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.

 926 GLY   ( 504-)  B    4.07

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.

3986 THR   ( 900-)  F    -3.1
1322 THR   ( 900-)  B    -3.1
 139 PRO   ( 383-)  A    -3.0
2137 PRO   ( 383-)  D    -3.0
3469 PRO   ( 383-)  F    -3.0
3320 THR   ( 900-)  E    -3.0
1471 PRO   ( 383-)  C    -3.0
 805 PRO   ( 383-)  B    -2.9
 656 THR   ( 900-)  A    -2.9
2654 THR   ( 900-)  D    -2.9
1988 THR   ( 900-)  C    -2.9
2803 PRO   ( 383-)  E    -2.9
1035 ILE   ( 613-)  B    -2.8
3699 ILE   ( 613-)  F    -2.7
3482 ARG   ( 396-)  F    -2.7
 944 SER   ( 522-)  B    -2.6
3790 VAL   ( 704-)  F    -2.6
2276 SER   ( 522-)  D    -2.6
 975 LEU   ( 553-)  B    -2.6
1007 LYS   ( 585-)  B    -2.6
3124 VAL   ( 704-)  E    -2.6
1641 LEU   ( 553-)  C    -2.6
 278 SER   ( 522-)  A    -2.6
3414 TRP   ( 328-)  F    -2.6
2973 LEU   ( 553-)  E    -2.5
And so on for a total of 146 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.

  30 ASN   ( 274-)  A  Poor phi/psi
  45 PHE   ( 289-)  A  omega poor
  47 ASN   ( 291-)  A  Poor phi/psi
  66 GLU   ( 310-)  A  Poor phi/psi
  75 ILE   ( 319-)  A  omega poor
  84 TRP   ( 328-)  A  Poor phi/psi
  86 GLN   ( 330-)  A  omega poor
  87 ASP   ( 331-)  A  omega poor
  94 ASN   ( 338-)  A  Poor phi/psi
 103 SER   ( 347-)  A  Poor phi/psi
 111 LEU   ( 355-)  A  omega poor
 114 SER   ( 358-)  A  omega poor
 115 TRP   ( 359-)  A  omega poor
 121 ASP   ( 365-)  A  Poor phi/psi
 138 TYR   ( 382-)  A  PRO omega poor
 153 ASN   ( 397-)  A  Poor phi/psi
 167 ASN   ( 411-)  A  Poor phi/psi
 194 ASN   ( 438-)  A  Poor phi/psi
 217 ASN   ( 461-)  A  Poor phi/psi
 219 ALA   ( 463-)  A  Poor phi/psi
 259 MET   ( 503-)  A  omega poor
 260 GLY   ( 504-)  A  Poor phi/psi
 268 TRP   ( 512-)  A  omega poor
 278 SER   ( 522-)  A  Poor phi/psi
 284 SER   ( 528-)  A  Poor phi/psi
And so on for a total of 329 lines.

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.

 240 VAL   ( 484-)  A    0.33
 906 VAL   ( 484-)  B    0.33
1572 VAL   ( 484-)  C    0.33
  16 SER   ( 260-)  A    0.36
3570 VAL   ( 484-)  F    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!

   3 LYS   ( 247-)  A      0
   7 VAL   ( 251-)  A      0
  10 ASP   ( 254-)  A      0
  30 ASN   ( 274-)  A      0
  40 PRO   ( 284-)  A      0
  41 ASP   ( 285-)  A      0
  54 ARG   ( 298-)  A      0
  55 ILE   ( 299-)  A      0
  56 PRO   ( 300-)  A      0
  58 GLN   ( 302-)  A      0
  65 GLU   ( 309-)  A      0
  66 GLU   ( 310-)  A      0
  67 PHE   ( 311-)  A      0
  68 VAL   ( 312-)  A      0
  69 GLN   ( 313-)  A      0
  76 THR   ( 320-)  A      0
  77 ASP   ( 321-)  A      0
  80 TYR   ( 324-)  A      0
  81 TYR   ( 325-)  A      0
  82 ASN   ( 326-)  A      0
  83 ALA   ( 327-)  A      0
  84 TRP   ( 328-)  A      0
  85 PRO   ( 329-)  A      0
  86 GLN   ( 330-)  A      0
  87 ASP   ( 331-)  A      0
And so on for a total of 2079 lines.

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!

2924 GLY   ( 504-)  E   1.64   20
1177 GLY   ( 755-)  B   1.63   13
1843 GLY   ( 755-)  C   1.62   14
3175 GLY   ( 755-)  E   1.51   13

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 379 PRO   ( 623-)  A    0.17 LOW
 802 PRO   ( 380-)  B    0.17 LOW
1178 PRO   ( 756-)  B    0.16 LOW
1255 PRO   ( 833-)  B    0.07 LOW
1711 PRO   ( 623-)  C    0.16 LOW
2377 PRO   ( 623-)  D    0.07 LOW
2587 PRO   ( 833-)  D    0.08 LOW
2907 PRO   ( 487-)  E    0.16 LOW
2977 PRO   ( 557-)  E    0.19 LOW
3573 PRO   ( 487-)  F    0.11 LOW

Warning: Unusual PRO puckering phases

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

  79 PRO   ( 323-)  A    26.6 half-chair N/C-delta (18 degrees)
 139 PRO   ( 383-)  A   -54.8 half-chair C-beta/C-alpha (-54 degrees)
 304 PRO   ( 548-)  A   -63.9 envelop C-beta (-72 degrees)
 422 PRO   ( 666-)  A  -112.8 envelop C-gamma (-108 degrees)
 543 PRO   ( 787-)  A    37.3 envelop C-delta (36 degrees)
 589 PRO   ( 833-)  A  -112.3 envelop C-gamma (-108 degrees)
 805 PRO   ( 383-)  B   -57.7 half-chair C-beta/C-alpha (-54 degrees)
 970 PRO   ( 548-)  B   -17.6 half-chair C-alpha/N (-18 degrees)
1209 PRO   ( 787-)  B    36.0 envelop C-delta (36 degrees)
1388 PRO   ( 300-)  C   105.0 envelop C-beta (108 degrees)
1471 PRO   ( 383-)  C   -46.5 half-chair C-beta/C-alpha (-54 degrees)
1636 PRO   ( 548-)  C   -63.8 envelop C-beta (-72 degrees)
1875 PRO   ( 787-)  C    31.4 envelop C-delta (36 degrees)
1921 PRO   ( 833-)  C  -117.1 half-chair C-delta/C-gamma (-126 degrees)
2077 PRO   ( 323-)  D    51.4 half-chair C-delta/C-gamma (54 degrees)
2137 PRO   ( 383-)  D   -54.0 half-chair C-beta/C-alpha (-54 degrees)
2541 PRO   ( 787-)  D    41.7 envelop C-delta (36 degrees)
2803 PRO   ( 383-)  E   -49.1 half-chair C-beta/C-alpha (-54 degrees)
2968 PRO   ( 548-)  E   -61.7 half-chair C-beta/C-alpha (-54 degrees)
3086 PRO   ( 666-)  E  -114.1 envelop C-gamma (-108 degrees)
3207 PRO   ( 787-)  E    25.9 half-chair N/C-delta (18 degrees)
3253 PRO   ( 833-)  E  -112.5 envelop C-gamma (-108 degrees)
3314 PRO   ( 894-)  E  -115.9 envelop C-gamma (-108 degrees)
3386 PRO   ( 300-)  F   102.1 envelop C-beta (108 degrees)
3409 PRO   ( 323-)  F    44.7 envelop C-delta (36 degrees)
3469 PRO   ( 383-)  F   -54.9 half-chair C-beta/C-alpha (-54 degrees)
3634 PRO   ( 548-)  F   -56.2 half-chair C-beta/C-alpha (-54 degrees)
3873 PRO   ( 787-)  F    35.4 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.

2017 ASN   ( 263-)  D      CB  <-> 4006 HOH   (2012 )  D      O      0.49    2.31  INTRA
1515 LEU   ( 427-)  C      N   <-> 1591 MET   ( 503-)  C      O      0.42    2.28  INTRA BL
2181 LEU   ( 427-)  D      N   <-> 2257 MET   ( 503-)  D      O      0.41    2.29  INTRA BL
 377 ARG   ( 621-)  A      CD  <-> 4003 HOH   (2307 )  A      O      0.39    2.41  INTRA
3317 ARG   ( 897-)  E      CZ  <-> 4007 HOH   (2451 )  E      O      0.34    2.46  INTRA
 183 LEU   ( 427-)  A      N   <->  259 MET   ( 503-)  A      O      0.32    2.38  INTRA BL
 790 THR   ( 368-)  B      CG2 <-> 4003 HOH   (2050 )  A      O      0.32    2.48  INTRA
 205 HIS   ( 449-)  A      CD2 <->  207 LEU   ( 451-)  A      N      0.32    2.78  INTRA BL
3707 ARG   ( 621-)  F      CD  <-> 4008 HOH   (2297 )  F      O      0.31    2.49  INTRA
3424 ASN   ( 338-)  F      ND2 <-> 4008 HOH   (2059 )  F      O      0.30    2.40  INTRA
2847 LEU   ( 427-)  E      N   <-> 2923 MET   ( 503-)  E      O      0.30    2.40  INTRA BL
2859 GLN   ( 439-)  E      NE2 <-> 4007 HOH   (2131 )  E      O      0.30    2.40  INTRA
1031 ARG   ( 609-)  B      NH2 <-> 1097 VAL   ( 675-)  B      O      0.30    2.40  INTRA
2150 ARG   ( 396-)  D      NH2 <-> 4006 HOH   (2118 )  D      O      0.30    2.40  INTRA
2404 ASN   ( 650-)  D      ND2 <-> 4006 HOH   (2323 )  D      O      0.28    2.42  INTRA
2219 THR   ( 465-)  D      CB  <-> 2244 GLN   ( 490-)  D      NE2    0.28    2.82  INTRA
 642 ASP   ( 886-)  A      OD2 <-> 1985 ARG   ( 897-)  C      NH1    0.27    2.43  INTRA
 406 ASN   ( 650-)  A      ND2 <-> 4003 HOH   (2325 )  A      O      0.26    2.44  INTRA
1043 ARG   ( 621-)  B      CD  <-> 4004 HOH   (2325 )  B      O      0.26    2.54  INTRA
3513 LEU   ( 427-)  F      N   <-> 3589 MET   ( 503-)  F      O      0.26    2.44  INTRA BL
2049 VAL   ( 295-)  D      CG1 <-> 2059 TYR   ( 305-)  D      CE2    0.26    2.94  INTRA BL
3317 ARG   ( 897-)  E      NE  <-> 4007 HOH   (2451 )  E      O      0.25    2.45  INTRA
3399 GLN   ( 313-)  F      OE1 <-> 3839 LYS   ( 753-)  F      NZ     0.25    2.45  INTRA
3041 ARG   ( 621-)  E      NH2 <-> 4007 HOH   (2253 )  E      O      0.25    2.45  INTRA
 912 GLN   ( 490-)  B      CG  <-> 4004 HOH   (2170 )  B      O      0.24    2.56  INTRA
And so on for a total of 365 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.

2052 ARG   ( 298-)  D      -6.45
1386 ARG   ( 298-)  C      -6.43
 720 ARG   ( 298-)  B      -6.43
3384 ARG   ( 298-)  F      -6.37
  54 ARG   ( 298-)  A      -6.25
2718 ARG   ( 298-)  E      -6.15
 367 ARG   ( 611-)  A      -5.98
1033 ARG   ( 611-)  B      -5.91
2520 TYR   ( 766-)  D      -5.74
1306 TYR   ( 884-)  B      -5.68
1749 TYR   ( 661-)  C      -5.66
 522 TYR   ( 766-)  A      -5.61
3697 ARG   ( 611-)  F      -5.59
1699 ARG   ( 611-)  C      -5.55
3031 ARG   ( 611-)  E      -5.53
 518 ARG   ( 762-)  A      -5.51
1854 TYR   ( 766-)  C      -5.49
1188 TYR   ( 766-)  B      -5.46
 640 TYR   ( 884-)  A      -5.45
3081 TYR   ( 661-)  E      -5.45
3970 TYR   ( 884-)  F      -5.42
2638 TYR   ( 884-)  D      -5.41
2769 ARG   ( 349-)  E      -5.39
3707 ARG   ( 621-)  F      -5.37
1437 ARG   ( 349-)  C      -5.36
And so on for a total of 61 lines.

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.

 666 THR   ( 910-)  A   -2.82
1527 GLN   ( 439-)  C   -2.73
2859 GLN   ( 439-)  E   -2.73
1596 HIS   ( 508-)  C   -2.70
2664 THR   ( 910-)  D   -2.64
1203 ASN   ( 781-)  B   -2.63
3145 ASN   ( 725-)  E   -2.61
1147 ASN   ( 725-)  B   -2.59
3811 ASN   ( 725-)  F   -2.58
2479 ASN   ( 725-)  D   -2.57
1813 ASN   ( 725-)  C   -2.55
3186 TYR   ( 766-)  E   -2.53
 481 ASN   ( 725-)  A   -2.52
  88 LYS   ( 332-)  A   -2.51
3852 TYR   ( 766-)  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.

 479 HIS   ( 723-)  A     -  482 PRO   ( 726-)  A        -1.49
1077 GLY   ( 655-)  B     - 1080 ASP   ( 658-)  B        -1.80
1145 HIS   ( 723-)  B     - 1148 PRO   ( 726-)  B        -1.55
1811 HIS   ( 723-)  C     - 1815 TRP   ( 727-)  C        -1.64
2409 GLY   ( 655-)  D     - 2412 ASP   ( 658-)  D        -1.76
2477 HIS   ( 723-)  D     - 2480 PRO   ( 726-)  D        -1.56
3143 HIS   ( 723-)  E     - 3147 TRP   ( 727-)  E        -1.67
3809 HIS   ( 723-)  F     - 3813 TRP   ( 727-)  F        -1.64

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.

4004 HOH   (2267 )  B      O
4005 HOH   (2301 )  C      O
4005 HOH   (2366 )  C      O
4006 HOH   (2376 )  D      O
4007 HOH   (2066 )  E      O
4007 HOH   (2307 )  E      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.

 123 GLN   ( 367-)  A
 142 ASN   ( 386-)  A
 153 ASN   ( 397-)  A
 195 GLN   ( 439-)  A
 201 HIS   ( 445-)  A
 205 HIS   ( 449-)  A
 217 ASN   ( 461-)  A
 237 ASN   ( 481-)  A
 244 ASN   ( 488-)  A
 245 GLN   ( 489-)  A
 256 ASN   ( 500-)  A
 264 HIS   ( 508-)  A
 298 HIS   ( 542-)  A
 317 ASN   ( 561-)  A
 326 GLN   ( 570-)  A
 381 ASN   ( 625-)  A
 384 HIS   ( 628-)  A
 443 ASN   ( 687-)  A
 488 ASN   ( 732-)  A
 499 HIS   ( 743-)  A
 527 ASN   ( 771-)  A
 588 ASN   ( 832-)  A
 609 GLN   ( 853-)  A
 626 ASN   ( 870-)  A
 789 GLN   ( 367-)  B
And so on for a total of 141 lines.

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.

  21 THR   ( 265-)  A      OG1
  38 SER   ( 282-)  A      N
  80 TYR   ( 324-)  A      N
  86 GLN   ( 330-)  A      NE2
 148 MET   ( 392-)  A      N
 181 ARG   ( 425-)  A      NH1
 195 GLN   ( 439-)  A      N
 239 THR   ( 483-)  A      OG1
 248 SER   ( 492-)  A      N
 252 ASN   ( 496-)  A      ND2
 256 ASN   ( 500-)  A      N
 371 GLN   ( 615-)  A      NE2
 401 SER   ( 645-)  A      OG
 404 ALA   ( 648-)  A      N
 418 LYS   ( 662-)  A      N
 434 TRP   ( 678-)  A      NE1
 447 GLN   ( 691-)  A      NE2
 455 ASN   ( 699-)  A      N
 478 ASP   ( 722-)  A      N
 486 GLY   ( 730-)  A      N
 544 ALA   ( 788-)  A      N
 562 SER   ( 806-)  A      OG
 575 GLY   ( 819-)  A      N
 635 ALA   ( 879-)  A      N
 653 ARG   ( 897-)  A      NE
And so on for a total of 141 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.

  82 ASN   ( 326-)  A      OD1
 106 HIS   ( 350-)  A      ND1
 184 HIS   ( 428-)  A      ND1
 283 HIS   ( 527-)  A      ND1
 748 ASN   ( 326-)  B      OD1
 772 HIS   ( 350-)  B      ND1
 850 HIS   ( 428-)  B      ND1
1414 ASN   ( 326-)  C      OD1
1438 HIS   ( 350-)  C      ND1
1516 HIS   ( 428-)  C      ND1
2080 ASN   ( 326-)  D      OD1
2165 ASN   ( 411-)  D      OD1
2182 HIS   ( 428-)  D      ND1
2256 HIS   ( 502-)  D      ND1
2770 HIS   ( 350-)  E      ND1
2848 HIS   ( 428-)  E      ND1
3412 ASN   ( 326-)  F      OD1
3436 HIS   ( 350-)  F      ND1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

4003 HOH   (2007 )  A      O  0.98  K  4 Ion-B
4003 HOH   (2169 )  A      O  0.85  K  5 ION-B
4003 HOH   (2361 )  A      O  0.95  K  4
4003 HOH   (2382 )  A      O  1.10  K  5
4003 HOH   (2414 )  A      O  0.99  K  4
4003 HOH   (2499 )  A      O  0.88  K  4 Ion-B
4004 HOH   (2100 )  B      O  0.89  K  4
4004 HOH   (2189 )  B      O  1.00  K  4
4004 HOH   (2261 )  B      O  1.11  K  4
4004 HOH   (2273 )  B      O  0.94  K  4 ION-B
4004 HOH   (2274 )  B      O  0.97  K  4
4004 HOH   (2298 )  B      O  0.86  K  5 Ion-B
4004 HOH   (2422 )  B      O  0.95  K  4
4005 HOH   (2098 )  C      O  0.94  K  4
4005 HOH   (2101 )  C      O  0.94  K  4 Ion-B
4005 HOH   (2392 )  C      O  0.89  K  4
4005 HOH   (2440 )  C      O  0.94  K  5
4006 HOH   (2100 )  D      O  1.06  K  4
4006 HOH   (2227 )  D      O  0.89  K  4 Ion-B
4006 HOH   (2236 )  D      O  1.13  K  4 Ion-B
4006 HOH   (2248 )  D      O  1.07  K  4
4007 HOH   (2039 )  E      O  0.99  K  4 Ion-B
4007 HOH   (2293 )  E      O  0.86  K  4
4007 HOH   (2337 )  E      O  1.07  K  4
4008 HOH   (2094 )  F      O  1.09  K  4
4008 HOH   (2100 )  F      O  0.86  K  4 Ion-B
4008 HOH   (2287 )  F      O  0.86  K  5 Ion-B
4008 HOH   (2362 )  F      O  1.08  K  5

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.

  20 ASP   ( 264-)  A   H-bonding suggests Asn
 120 ASP   ( 364-)  A   H-bonding suggests Asn; but Alt-Rotamer
 446 ASP   ( 690-)  A   H-bonding suggests Asn; but Alt-Rotamer
 786 ASP   ( 364-)  B   H-bonding suggests Asn; but Alt-Rotamer
1034 ASP   ( 612-)  B   H-bonding suggests Asn; but Alt-Rotamer
1112 ASP   ( 690-)  B   H-bonding suggests Asn; but Alt-Rotamer
1452 ASP   ( 364-)  C   H-bonding suggests Asn; but Alt-Rotamer
1664 GLU   ( 576-)  C   H-bonding suggests Gln
1778 ASP   ( 690-)  C   H-bonding suggests Asn; but Alt-Rotamer
2118 ASP   ( 364-)  D   H-bonding suggests Asn; but Alt-Rotamer
2444 ASP   ( 690-)  D   H-bonding suggests Asn; but Alt-Rotamer
2684 ASP   ( 264-)  E   H-bonding suggests Asn; but Alt-Rotamer
2784 ASP   ( 364-)  E   H-bonding suggests Asn; but Alt-Rotamer
3032 ASP   ( 612-)  E   H-bonding suggests Asn; but Alt-Rotamer
3110 ASP   ( 690-)  E   H-bonding suggests Asn; but Alt-Rotamer
3450 ASP   ( 364-)  F   H-bonding suggests Asn; but Alt-Rotamer
3776 ASP   ( 690-)  F   H-bonding suggests Asn; but Alt-Rotamer

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 :   0.075
  2nd generation packing quality :  -1.212
  Ramachandran plot appearance   :  -0.705
  chi-1/chi-2 rotamer normality  :  -1.437
  Backbone conformation          :  -0.665

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.511 (tight)
  Bond angles                    :   0.786
  Omega angle restraints         :   1.245
  Side chain planarity           :   0.554 (tight)
  Improper dihedral distribution :   0.857
  B-factor distribution          :   0.464
  Inside/Outside distribution    :   1.040

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.511 (tight)
  Bond angles                    :   0.786
  Omega angle restraints         :   1.245
  Side chain planarity           :   0.554 (tight)
  Improper dihedral distribution :   0.857
  B-factor distribution          :   0.464
  Inside/Outside distribution    :   1.040
==============

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.