WHAT IF Check report

This file was created 2012-01-31 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 pdb2rus.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 883 FOR   ( 501-)  A  -         Size
 885 FOR   ( 501-)  B  -         Size

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

 181 LYS   ( 191-)  A  -   NZ  bound to  883 FOR   ( 501-)  A  -   C
 617 LYS   ( 191-)  B  -   NZ  bound to  885 FOR   ( 501-)  B  -   C

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  54 THR   (  64-)  A  -   CB
  54 THR   (  64-)  A  -   OG1
  54 THR   (  64-)  A  -   CG2
 314 THR   ( 324-)  A  -   CB
 314 THR   ( 324-)  A  -   OG1
 314 THR   ( 324-)  A  -   CG2
 438 GLN   (   3-)  B  -   CB
 438 GLN   (   3-)  B  -   CG
 438 GLN   (   3-)  B  -   CD
 438 GLN   (   3-)  B  -   OE1
 438 GLN   (   3-)  B  -   NE2
 489 ASN   (  54-)  B  -   CB
 489 ASN   (  54-)  B  -   CG
 489 ASN   (  54-)  B  -   OD1
 489 ASN   (  54-)  B  -   ND2
 490 THR   (  64-)  B  -   CB
 490 THR   (  64-)  B  -   OG1
 490 THR   (  64-)  B  -   CG2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

  54 THR   (  64-)  A  -   N
  54 THR   (  64-)  A  -   CA
  54 THR   (  64-)  A  -   C
  54 THR   (  64-)  A  -   O
 314 THR   ( 324-)  A  -   N
 314 THR   ( 324-)  A  -   CA
 314 THR   ( 324-)  A  -   C
 314 THR   ( 324-)  A  -   O
 438 GLN   (   3-)  B  -   N
 438 GLN   (   3-)  B  -   CA
 438 GLN   (   3-)  B  -   C
 438 GLN   (   3-)  B  -   O
 489 ASN   (  54-)  B  -   N
 489 ASN   (  54-)  B  -   CA
 489 ASN   (  54-)  B  -   C
 489 ASN   (  54-)  B  -   O
 490 THR   (  64-)  B  -   N
 490 THR   (  64-)  B  -   CA
 490 THR   (  64-)  B  -   C
 490 THR   (  64-)  B  -   O
 756 GLY   ( 332-)  B  -   N
 756 GLY   ( 332-)  B  -   CA
 756 GLY   ( 332-)  B  -   C
 756 GLY   ( 332-)  B  -   O

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

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

Warning: What type of B-factor?

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

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

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

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

   5 ARG   (   6-)  A
  68 ARG   (  78-)  A
  82 ARG   (  92-)  A
 123 ARG   ( 133-)  A
 142 ARG   ( 152-)  A
 162 ARG   ( 172-)  A
 195 ARG   ( 205-)  A
 206 ARG   ( 216-)  A
 207 ARG   ( 217-)  A
 233 ARG   ( 243-)  A
 266 ARG   ( 276-)  A
 267 ARG   ( 277-)  A
 268 ARG   ( 278-)  A
 291 ARG   ( 301-)  A
 317 ARG   ( 337-)  A
 334 ARG   ( 354-)  A
 355 ARG   ( 375-)  A
 388 ARG   ( 408-)  A
 391 ARG   ( 411-)  A
 398 ARG   ( 418-)  A
 408 ARG   ( 428-)  A
 415 ARG   ( 435-)  A
 432 ARG   ( 452-)  A
 441 ARG   (   6-)  B
 504 ARG   (  78-)  B
 518 ARG   (  92-)  B
 559 ARG   ( 133-)  B
 578 ARG   ( 152-)  B
 598 ARG   ( 172-)  B
 631 ARG   ( 205-)  B
 642 ARG   ( 216-)  B
 643 ARG   ( 217-)  B
 669 ARG   ( 243-)  B
 702 ARG   ( 276-)  B
 703 ARG   ( 277-)  B
 704 ARG   ( 278-)  B
 714 ARG   ( 288-)  B
 727 ARG   ( 301-)  B
 739 ARG   ( 313-)  B
 778 ARG   ( 354-)  B
 799 ARG   ( 375-)  B
 832 ARG   ( 408-)  B
 835 ARG   ( 411-)  B
 842 ARG   ( 418-)  B
 852 ARG   ( 428-)  B
 859 ARG   ( 435-)  B
 876 ARG   ( 452-)  B

Warning: Tyrosine convention problem

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

  27 TYR   (  28-)  A
  35 TYR   (  36-)  A
  37 TYR   (  38-)  A
 117 TYR   ( 127-)  A
 122 TYR   ( 132-)  A
 293 TYR   ( 303-)  A
 321 TYR   ( 341-)  A
 333 TYR   ( 353-)  A
 406 TYR   ( 426-)  A
 428 TYR   ( 448-)  A
 442 TYR   (   7-)  B
 463 TYR   (  28-)  B
 498 TYR   (  72-)  B
 558 TYR   ( 132-)  B
 672 TYR   ( 246-)  B
 729 TYR   ( 303-)  B
 765 TYR   ( 341-)  B
 850 TYR   ( 426-)  B

Warning: Phenylalanine convention problem

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

  44 PHE   (  45-)  A
  94 PHE   ( 104-)  A
 116 PHE   ( 126-)  A
 126 PHE   ( 136-)  A
 173 PHE   ( 183-)  A
 191 PHE   ( 201-)  A
 228 PHE   ( 238-)  A
 241 PHE   ( 251-)  A
 269 PHE   ( 279-)  A
 273 PHE   ( 283-)  A
 359 PHE   ( 379-)  A
 377 PHE   ( 397-)  A
 420 PHE   ( 440-)  A
 480 PHE   (  45-)  B
 516 PHE   (  90-)  B
 552 PHE   ( 126-)  B
 602 PHE   ( 176-)  B
 627 PHE   ( 201-)  B
 709 PHE   ( 283-)  B
 732 PHE   ( 306-)  B
 753 PHE   ( 327-)  B
 864 PHE   ( 440-)  B

Warning: Aspartic acid convention problem

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

  15 ASP   (  16-)  A
  58 ASP   (  68-)  A
 178 ASP   ( 188-)  A
 183 ASP   ( 193-)  A
 203 ASP   ( 213-)  A
 225 ASP   ( 235-)  A
 226 ASP   ( 236-)  A
 271 ASP   ( 281-)  A
 316 ASP   ( 336-)  A
 326 ASP   ( 346-)  A
 405 ASP   ( 425-)  A
 423 ASP   ( 443-)  A
 451 ASP   (  16-)  B
 494 ASP   (  68-)  B
 501 ASP   (  75-)  B
 517 ASP   (  91-)  B
 522 ASP   (  96-)  B
 563 ASP   ( 137-)  B
 619 ASP   ( 193-)  B
 639 ASP   ( 213-)  B
 661 ASP   ( 235-)  B
 770 ASP   ( 346-)  B
 825 ASP   ( 401-)  B
 843 ASP   ( 419-)  B
 849 ASP   ( 425-)  B
 867 ASP   ( 443-)  B

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.

  21 GLU   (  22-)  A
  47 GLU   (  48-)  A
  66 GLU   (  76-)  A
  69 GLU   (  79-)  A
 109 GLU   ( 119-)  A
 120 GLU   ( 130-)  A
 184 GLU   ( 194-)  A
 214 GLU   ( 224-)  A
 229 GLU   ( 239-)  A
 243 GLU   ( 253-)  A
 327 GLU   ( 347-)  A
 450 GLU   (  15-)  B
 483 GLU   (  48-)  B
 499 GLU   (  73-)  B
 502 GLU   (  76-)  B
 505 GLU   (  79-)  B
 650 GLU   ( 224-)  B
 671 GLU   ( 245-)  B
 757 GLU   ( 333-)  B
 771 GLU   ( 347-)  B
 853 GLU   ( 429-)  B
 856 GLU   ( 432-)  B

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.

 344 THR   ( 364-)  A      CA   CB    1.61    4.2
 755 LYS   ( 329-)  B      N   -C     1.22   -5.2
 881 VAL   ( 457-)  B      C    O     1.31    4.1

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

 |  0.995695  0.000283  0.000860|
 |  0.000283  0.998390 -0.000084|
 |  0.000860 -0.000084  0.997223|
Proposed new scale matrix

 |  0.015333 -0.000004  0.000548|
 | -0.000004  0.014187  0.000001|
 | -0.000008  0.000000  0.009640|
With corresponding cell

    A    =  65.219  B   =  70.488  C    = 103.800
    Alpha=  90.007  Beta=  91.999  Gamma=  89.968

The CRYST1 cell dimensions

    A    =  65.500  B   =  70.600  C    = 104.100
    Alpha=  90.000  Beta=  92.100  Gamma=  90.000

Variance: 251.954
(Under-)estimated Z-score: 11.698

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.

   1 ASP   (   2-)  A      CA   CB   CG  118.78    6.2
   2 GLN   (   3-)  A      CA   C    O   136.96    9.5
   2 GLN   (   3-)  A      N    CA   CB  121.97    6.7
   2 GLN   (   3-)  A      CA   CB   CG  123.72    4.8
   3 SER   (   4-)  A     -CA  -C    N   105.58   -5.3
   3 SER   (   4-)  A     -C    N    CA  134.22    7.0
   3 SER   (   4-)  A      N    CA   C    94.48   -6.0
   4 SER   (   5-)  A     -CA  -C    N   124.32    4.1
   4 SER   (   5-)  A      CA   CB   OG  119.97    4.4
   8 ASN   (   9-)  A      C    CA   CB  120.24    5.3
   8 ASN   (   9-)  A      CA   CB   CG  121.19    8.6
   9 LEU   (  10-)  A     -CA  -C    N   107.01   -4.6
   9 LEU   (  10-)  A      N    CA   C    94.25   -6.1
   9 LEU   (  10-)  A      CA   C    O   107.38   -7.9
   9 LEU   (  10-)  A      N    CA   CB  102.69   -4.6
  10 ALA   (  11-)  A     -CA  -C    N   126.77    5.3
  10 ALA   (  11-)  A      N    CA   CB  118.99    5.7
  13 GLU   (  14-)  A      CB   CG   CD  121.26    5.1
  14 GLU   (  15-)  A      CG   CD   OE2 108.28   -4.4
  22 HIS   (  23-)  A      N    CA   CB  119.06    5.0
  23 VAL   (  24-)  A      N    CA   C    99.21   -4.3
  23 VAL   (  24-)  A      C    CA   CB  118.41    4.4
  24 LEU   (  25-)  A      C    CA   CB  123.10    6.8
  28 ILE   (  29-)  A      N    CA   C    99.60   -4.1
  35 TYR   (  36-)  A     -C    N    CA  128.96    4.0
And so on for a total of 483 lines.

Error: Nomenclature error(s)

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

   5 ARG   (   6-)  A
  15 ASP   (  16-)  A
  21 GLU   (  22-)  A
  47 GLU   (  48-)  A
  58 ASP   (  68-)  A
  66 GLU   (  76-)  A
  68 ARG   (  78-)  A
  69 GLU   (  79-)  A
  82 ARG   (  92-)  A
 109 GLU   ( 119-)  A
 120 GLU   ( 130-)  A
 123 ARG   ( 133-)  A
 142 ARG   ( 152-)  A
 162 ARG   ( 172-)  A
 178 ASP   ( 188-)  A
 183 ASP   ( 193-)  A
 184 GLU   ( 194-)  A
 195 ARG   ( 205-)  A
 203 ASP   ( 213-)  A
 206 ARG   ( 216-)  A
 207 ARG   ( 217-)  A
 214 GLU   ( 224-)  A
 225 ASP   ( 235-)  A
 226 ASP   ( 236-)  A
 229 GLU   ( 239-)  A
And so on for a total of 95 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.

  54 THR   (  64-)  A      C     15.6    23.71     0.30
 313 GLY   ( 323-)  A      C      8.3    11.08     0.06
 535 MET   ( 109-)  B      CA     6.8    46.33    34.17
The average deviation= 1.617

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.

 692 VAL   ( 266-)  B    7.57
   9 LEU   (  10-)  A    6.90
 423 ASP   ( 443-)  A    6.83
 106 GLY   ( 116-)  A    6.74
 697 ALA   ( 271-)  B    6.56
 422 GLY   ( 442-)  A    6.55
   3 SER   (   4-)  A    6.53
 647 GLU   ( 221-)  B    6.11
 768 THR   ( 344-)  B    5.76
 254 GLY   ( 264-)  A    5.46
 259 ALA   ( 269-)  A    5.43
 534 THR   ( 108-)  B    5.42
 440 SER   (   5-)  B    5.37
 731 ALA   ( 305-)  B    5.24
 665 GLU   ( 239-)  B    5.18
 324 THR   ( 344-)  A    5.09
 441 ARG   (   6-)  B    5.04
 793 GLY   ( 369-)  B    5.00
 693 ALA   ( 267-)  B    4.96
 778 ARG   ( 354-)  B    4.91
 384 VAL   ( 404-)  A    4.80
  44 PHE   (  45-)  A    4.80
 343 CYS   ( 363-)  A    4.79
 835 ARG   ( 411-)  B    4.77
 319 ILE   ( 339-)  A    4.74
And so on for a total of 52 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 : 2.062

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.093

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.

  52 THR   (  53-)  A    -3.6
 753 PHE   ( 327-)  B    -3.5
 589 THR   ( 163-)  B    -3.1
 429 PRO   ( 449-)  A    -3.1
 748 THR   ( 322-)  B    -3.0
 153 THR   ( 163-)  A    -2.8
 599 PRO   ( 173-)  B    -2.7
  55 ARG   (  65-)  A    -2.6
   4 SER   (   5-)  A    -2.4
 371 THR   ( 391-)  A    -2.4
 536 GLY   ( 110-)  B    -2.4
 643 ARG   ( 217-)  B    -2.4
 873 PRO   ( 449-)  B    -2.4
 159 LEU   ( 169-)  A    -2.4
 749 GLY   ( 323-)  B    -2.4
 430 GLY   ( 450-)  A    -2.4
 791 ILE   ( 367-)  B    -2.3
 431 TRP   ( 451-)  A    -2.3
 132 ASN   ( 142-)  A    -2.3
 760 ASP   ( 336-)  B    -2.3
 185 PRO   ( 195-)  A    -2.3
 595 LEU   ( 169-)  B    -2.3
 156 LYS   ( 166-)  A    -2.3
 338 GLY   ( 358-)  A    -2.3
 678 GLY   ( 252-)  B    -2.2
And so on for a total of 53 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.

   3 SER   (   4-)  A  Poor phi/psi
   4 SER   (   5-)  A  Poor phi/psi
  10 ALA   (  11-)  A  Poor phi/psi
  20 GLY   (  21-)  A  Poor phi/psi
  32 LYS   (  33-)  A  Poor phi/psi
  33 ALA   (  34-)  A  Poor phi/psi
  49 SER   (  50-)  A  Poor phi/psi
  52 THR   (  53-)  A  Poor phi/psi
  56 GLY   (  66-)  A  Poor phi/psi
  69 GLU   (  79-)  A  Poor phi/psi
 104 GLY   ( 114-)  A  Poor phi/psi
 107 ASP   ( 117-)  A  Poor phi/psi
 132 ASN   ( 142-)  A  Poor phi/psi
 146 ASP   ( 156-)  A  Poor phi/psi
 156 LYS   ( 166-)  A  PRO omega poor
 176 GLY   ( 186-)  A  Poor phi/psi
 254 GLY   ( 264-)  A  Poor phi/psi
 279 ALA   ( 289-)  A  Poor phi/psi
 282 GLY   ( 292-)  A  Poor phi/psi
 306 GLY   ( 316-)  A  Poor phi/psi
 332 PHE   ( 352-)  A  Poor phi/psi
 338 GLY   ( 358-)  A  Poor phi/psi
 367 ASN   ( 387-)  A  Poor phi/psi
 423 ASP   ( 443-)  A  Poor phi/psi
 430 GLY   ( 450-)  A  Poor phi/psi
 431 TRP   ( 451-)  A  Poor phi/psi
 439 SER   (   4-)  B  Poor phi/psi
 440 SER   (   5-)  B  Poor phi/psi
 485 SER   (  50-)  B  Poor phi/psi
 488 THR   (  53-)  B  Poor phi/psi
 491 ARG   (  65-)  B  Poor phi/psi
 505 GLU   (  79-)  B  Poor phi/psi
 536 GLY   ( 110-)  B  Poor phi/psi
 542 GLY   ( 116-)  B  Poor phi/psi
 546 TYR   ( 120-)  B  Poor phi/psi
 551 ASP   ( 125-)  B  Poor phi/psi
 568 ASN   ( 142-)  B  Poor phi/psi
 582 ASP   ( 156-)  B  Poor phi/psi
 592 LYS   ( 166-)  B  PRO omega poor
 612 GLY   ( 186-)  B  Poor phi/psi
 742 GLY   ( 316-)  B  Poor phi/psi
 748 THR   ( 322-)  B  Poor phi/psi
 749 GLY   ( 323-)  B  Poor phi/psi
 751 MET   ( 325-)  B  Poor phi/psi
 753 PHE   ( 327-)  B  Poor phi/psi
 757 GLU   ( 333-)  B  Poor phi/psi
 758 SER   ( 334-)  B  Poor phi/psi
 760 ASP   ( 336-)  B  Poor phi/psi
 811 ASN   ( 387-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.379

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.379

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 SER   (   4-)  A      0
   6 TYR   (   7-)  A      0
   7 VAL   (   8-)  A      0
   8 ASN   (   9-)  A      0
   9 LEU   (  10-)  A      0
  10 ALA   (  11-)  A      0
  21 GLU   (  22-)  A      0
  22 HIS   (  23-)  A      0
  32 LYS   (  33-)  A      0
  33 ALA   (  34-)  A      0
  35 TYR   (  36-)  A      0
  48 SER   (  49-)  A      0
  49 SER   (  50-)  A      0
  50 THR   (  51-)  A      0
  52 THR   (  53-)  A      0
  53 ASN   (  54-)  A      0
  54 THR   (  64-)  A      0
  55 ARG   (  65-)  A      0
  57 VAL   (  67-)  A      0
  62 TYR   (  72-)  A      0
  63 GLU   (  73-)  A      0
  70 LEU   (  80-)  A      0
  80 PHE   (  90-)  A      0
  83 ASN   (  93-)  A      0
  85 THR   (  95-)  A      0
And so on for a total of 309 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 : 1.984

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!

 106 GLY   ( 116-)  A   3.22   11
 422 GLY   ( 442-)  A   3.19   80
 540 GLY   ( 114-)  B   1.72   12
 626 PRO   ( 200-)  B   1.65   10

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]

 143 PRO   ( 153-)  A    0.07 LOW
 157 PRO   ( 167-)  A    0.19 LOW
 163 PRO   ( 173-)  A    0.50 HIGH
 165 PRO   ( 175-)  A    0.50 HIGH
 193 PRO   ( 203-)  A    0.12 LOW
 227 PRO   ( 237-)  A    0.46 HIGH
 467 PRO   (  32-)  B    0.18 LOW
 579 PRO   ( 153-)  B    0.15 LOW
 621 PRO   ( 195-)  B    0.14 LOW
 663 PRO   ( 237-)  B    0.50 HIGH
 775 PRO   ( 351-)  B    0.02 LOW
 873 PRO   ( 449-)  B    0.51 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].

 185 PRO   ( 195-)  A   -52.3 half-chair C-beta/C-alpha (-54 degrees)
 190 PRO   ( 200-)  A  -126.7 half-chair C-delta/C-gamma (-126 degrees)
 383 PRO   ( 403-)  A     7.4 envelop N (0 degrees)
 402 PRO   ( 422-)  A    38.8 envelop C-delta (36 degrees)
 429 PRO   ( 449-)  A   111.5 envelop C-beta (108 degrees)
 626 PRO   ( 200-)  B    47.0 half-chair C-delta/C-gamma (54 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.

 418 GLU   ( 438-)  A      OE2 <->  437 VAL   ( 457-)  A      CG2    0.54    2.26  INTRA BF
 120 GLU   ( 130-)  A      OE1 <->  123 ARG   ( 133-)  A      NH2    0.47    2.23  INTRA
 391 ARG   ( 411-)  A      NH2 <->  886 HOH   ( 556 )  A      O      0.40    2.30  INTRA BF
 578 ARG   ( 152-)  B      NH1 <->  887 HOH   ( 693 )  B      O      0.40    2.30  INTRA
 538 ASN   ( 112-)  B      ND2 <->  887 HOH   ( 873 )  B      O      0.39    2.31  INTRA BF
  52 THR   (  53-)  A      O   <->   53 ASN   (  54-)  A      CB     0.37    2.23  INTRA
 757 GLU   ( 333-)  B      CG  <->  758 SER   ( 334-)  B      N      0.33    2.67  INTRA
 195 ARG   ( 205-)  A      NE  <->  886 HOH   ( 752 )  A      O      0.30    2.40  INTRA BF
  43 HIS   (  44-)  A      ND1 <->  107 ASP   ( 117-)  A      OD2    0.30    2.40  INTRA
 466 LYS   (  31-)  B      NZ  <->  545 GLU   ( 119-)  B      OE2    0.30    2.40  INTRA BF
 642 ARG   ( 216-)  B      NH2 <->  679 GLU   ( 253-)  B      OE2    0.29    2.41  INTRA
 578 ARG   ( 152-)  B      NH2 <->  585 LEU   ( 159-)  B      O      0.28    2.42  INTRA BL
 435 LEU   ( 455-)  A      C   <->  437 VAL   ( 457-)  A      N      0.25    2.65  INTRA BF
   3 SER   (   4-)  A      O   <->    5 ARG   (   6-)  A      N      0.24    2.46  INTRA
 588 GLY   ( 162-)  B      N   <->  814 LEU   ( 390-)  B      O      0.24    2.46  INTRA BL
 300 LYS   ( 310-)  A      NZ  <->  886 HOH   ( 508 )  A      O      0.23    2.47  INTRA BL
 195 ARG   ( 205-)  A      NH2 <->  886 HOH   ( 579 )  A      O      0.23    2.47  INTRA
 431 TRP   ( 451-)  A      O   <->  435 LEU   ( 455-)  A      N      0.23    2.47  INTRA BF
 823 HIS   ( 399-)  B      ND1 <->  825 ASP   ( 401-)  B      N      0.22    2.78  INTRA
 739 ARG   ( 313-)  B      NH2 <->  784 MET   ( 360-)  B      O      0.22    2.48  INTRA BL
 850 TYR   ( 426-)  B      O   <->  854 HIS   ( 430-)  B      ND1    0.21    2.49  INTRA
 598 ARG   ( 172-)  B      NE  <->  627 PHE   ( 201-)  B      O      0.21    2.49  INTRA
 591 ILE   ( 165-)  B      CG2 <->  602 PHE   ( 176-)  B      CE1    0.21    2.99  INTRA
 408 ARG   ( 428-)  A      NE  <->  434 ALA   ( 454-)  A      O      0.21    2.49  INTRA BF
  68 ARG   (  78-)  A      NE  <->  886 HOH   ( 603 )  A      O      0.21    2.49  INTRA BF
And so on for a total of 211 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

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.

 753 PHE   ( 327-)  B      -7.21
 751 MET   ( 325-)  B      -6.40
  55 ARG   (  65-)  A      -5.92
 757 GLU   ( 333-)  B      -5.84
 714 ARG   ( 288-)  B      -5.77
 842 ARG   ( 418-)  B      -5.65
 398 ARG   ( 418-)  A      -5.48
 247 HIS   ( 257-)  A      -5.39
 704 ARG   ( 278-)  B      -5.37
 156 LYS   ( 166-)  A      -5.35
 362 ASN   ( 382-)  A      -5.33
 268 ARG   ( 278-)  A      -5.29
 103 GLN   ( 113-)  A      -5.28
 683 HIS   ( 257-)  B      -5.28
 145 VAL   ( 155-)  A      -5.22
 870 GLN   ( 446-)  B      -5.20
 806 ASN   ( 382-)  B      -5.19
 329 GLN   ( 349-)  A      -5.16
 305 GLN   ( 315-)  A      -5.06
 380 ILE   ( 400-)  A      -5.01
 581 VAL   ( 155-)  B      -5.00

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.

 751 MET   ( 325-)  B       754 - GLY    328- ( B)         -5.57
 756 GLY   ( 332-)  B       759 - SER    335- ( B)         -4.68

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

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.

 365 ASN   ( 385-)  A   -2.55
 283 ALA   ( 293-)  A   -2.50

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

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

 886 HOH   ( 755 )  A      O

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 886 HOH   ( 504 )  A      O     76.93    8.28   -4.70
 886 HOH   ( 506 )  A      O     42.35   40.24   18.34
 886 HOH   ( 530 )  A      O     45.77   28.59   57.46
 886 HOH   ( 554 )  A      O     35.14   -9.62   41.32
 886 HOH   ( 557 )  A      O     33.26  -16.67   42.81
 886 HOH   ( 559 )  A      O     39.92   27.34   60.98
 886 HOH   ( 567 )  A      O     23.52   -4.76   43.80
 886 HOH   ( 569 )  A      O     42.89   23.37   65.90
 886 HOH   ( 588 )  A      O     11.74   18.58   64.95
 886 HOH   ( 599 )  A      O     34.40  -16.56   39.69
 886 HOH   ( 609 )  A      O      8.12   29.17   46.93
 886 HOH   ( 615 )  A      O     48.89   28.83   59.60
 886 HOH   ( 616 )  A      O     56.10   40.87   30.18
 886 HOH   ( 617 )  A      O     44.06   11.44   -9.55
 886 HOH   ( 618 )  A      O     77.24   -6.15    9.25
 886 HOH   ( 623 )  A      O     46.76   36.31   37.97
 886 HOH   ( 625 )  A      O      2.56   15.16   62.67
 886 HOH   ( 629 )  A      O     35.96   38.35   36.13
 886 HOH   ( 642 )  A      O     12.75   11.21   65.05
 886 HOH   ( 646 )  A      O     25.33   26.55   52.13
 886 HOH   ( 656 )  A      O     53.60   28.04   50.43
 886 HOH   ( 661 )  A      O     62.49  -15.05   33.96
 886 HOH   ( 675 )  A      O     23.96   25.60   54.18
 886 HOH   ( 690 )  A      O     70.01    2.95   31.78
 886 HOH   ( 695 )  A      O     20.47    8.61   66.80
And so on for a total of 107 lines.

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.

 886 HOH   ( 504 )  A      O
 886 HOH   ( 518 )  A      O
 886 HOH   ( 529 )  A      O
 886 HOH   ( 536 )  A      O
 886 HOH   ( 539 )  A      O
 886 HOH   ( 569 )  A      O
 886 HOH   ( 573 )  A      O
 886 HOH   ( 609 )  A      O
 886 HOH   ( 616 )  A      O
 886 HOH   ( 623 )  A      O
 886 HOH   ( 626 )  A      O
 886 HOH   ( 632 )  A      O
 886 HOH   ( 656 )  A      O
 886 HOH   ( 659 )  A      O
 886 HOH   ( 685 )  A      O
 886 HOH   ( 688 )  A      O
 886 HOH   ( 695 )  A      O
 886 HOH   ( 714 )  A      O
 886 HOH   ( 719 )  A      O
 886 HOH   ( 723 )  A      O
 886 HOH   ( 735 )  A      O
 886 HOH   ( 739 )  A      O
 886 HOH   ( 753 )  A      O
 886 HOH   ( 754 )  A      O
 886 HOH   ( 755 )  A      O
And so on for a total of 85 lines.

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.

   8 ASN   (   9-)  A
  22 HIS   (  23-)  A
  83 ASN   (  93-)  A
 101 ASN   ( 111-)  A
 114 HIS   ( 124-)  A
 132 ASN   ( 142-)  A
 209 GLN   ( 219-)  A
 298 HIS   ( 308-)  A
 311 HIS   ( 321-)  A
 329 GLN   ( 349-)  A
 458 HIS   (  23-)  B
 683 HIS   ( 257-)  B
 734 HIS   ( 308-)  B
 773 GLN   ( 349-)  B
 811 ASN   ( 387-)  B

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.

   7 VAL   (   8-)  A      N
  14 GLU   (  15-)  A      N
  35 TYR   (  36-)  A      N
  39 ALA   (  40-)  A      N
  57 VAL   (  67-)  A      N
  93 SER   ( 103-)  A      N
  93 SER   ( 103-)  A      OG
 122 TYR   ( 132-)  A      N
 147 GLY   ( 157-)  A      N
 149 LEU   ( 159-)  A      N
 191 PHE   ( 201-)  A      N
 219 SER   ( 229-)  A      OG
 233 ARG   ( 243-)  A      NH1
 254 GLY   ( 264-)  A      N
 257 ALA   ( 267-)  A      N
 261 ALA   ( 271-)  A      N
 278 ARG   ( 288-)  A      N
 278 ARG   ( 288-)  A      NE
 285 THR   ( 295-)  A      OG1
 286 SER   ( 296-)  A      N
 290 LYS   ( 300-)  A      N
 291 ARG   ( 301-)  A      NE
 293 TYR   ( 303-)  A      N
 294 THR   ( 304-)  A      OG1
 313 GLY   ( 323-)  A      N
And so on for a total of 72 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.

 103 GLN   ( 113-)  A      OE1
 144 GLU   ( 154-)  A      OE1
 253 ASP   ( 263-)  A      OD1
 494 ASP   (  68-)  B      OD2
 537 ASN   ( 111-)  B      OD1
 539 GLN   ( 113-)  B      OE1
 607 HIS   ( 181-)  B      ND1
 620 GLU   ( 194-)  B      OE1

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 ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 882  MG   ( 500-)  A     0.28   0.91 Could be  K (Few ligands (4) )
 884  MG   ( 500-)  B   -.-  -.-  Too few ligands (3)

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.

 886 HOH   ( 557 )  A      O  0.90  K  4 Ion-B
 886 HOH   ( 585 )  A      O  0.86  K  4 Ion-B
 886 HOH   ( 679 )  A      O  1.10  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.

 144 GLU   ( 154-)  A   H-bonding suggests Gln
 211 GLU   ( 221-)  A   H-bonding suggests Gln
 253 ASP   ( 263-)  A   H-bonding suggests Asn
 327 GLU   ( 347-)  A   H-bonding suggests Gln
 543 ASP   ( 117-)  B   H-bonding suggests Asn
 646 ASP   ( 220-)  B   H-bonding suggests Asn
 689 ASP   ( 263-)  B   H-bonding suggests Asn; but Alt-Rotamer
 853 GLU   ( 429-)  B   H-bonding suggests Gln
 869 ASP   ( 445-)  B   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 :  -0.944
  2nd generation packing quality :  -2.111
  Ramachandran plot appearance   :  -3.093 (poor)
  chi-1/chi-2 rotamer normality  :  -4.379 (bad)
  Backbone conformation          :  -0.211

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.802
  Bond angles                    :   1.969
  Omega angle restraints         :   0.361 (tight)
  Side chain planarity           :   0.768
  Improper dihedral distribution :   1.432
  B-factor distribution          :   0.569
  Inside/Outside distribution    :   0.997

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.802
  Bond angles                    :   1.969
  Omega angle restraints         :   0.361 (tight)
  Side chain planarity           :   0.768
  Improper dihedral distribution :   1.432
  B-factor distribution          :   0.569
  Inside/Outside distribution    :   0.997
==============

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

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

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

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

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

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

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

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

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

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

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

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

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

    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.