WHAT IF Check report

This file was created 2012-04-12 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 pdb2xy9.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some 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 two or less which PRODRUG also cannot cope with), 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.

 589 3ES   (1635-)  A  -
 590 3ES   (1636-)  A  -
 591 EPE   (1634-)  A  -         OK
 592 BMA   (1633-)  A  -         OK
 593 ACT   (1625-)  A  -         OK

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.

 582 NAG   (1629-)  A  -   O4  bound to  583 NAG   (1630-)  A  -   C1
 583 NAG   (1630-)  A  -   O4  bound to  592 BMA   (1633-)  A  -   C1

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  25 GLU   (  64-)  A      CG
  25 GLU   (  64-)  A      CD
  25 GLU   (  64-)  A      OE1
  25 GLU   (  64-)  A      OE2
 259 SER   ( 298-)  A      OG
 397 ASP   ( 440-)  A      CG
 397 ASP   ( 440-)  A      OD1
 397 ASP   ( 440-)  A      OD2

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

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.

 113 CYS   ( 152-)  A      SG  -SG*   2.29    6.3
 119 CYS   ( 158-)  A      SG  -SG*   2.29    6.3

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: 0.378
RMS-deviation in bond distances: 0.010

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

 |  0.997181 -0.000005 -0.000258|
 | -0.000005  0.997103  0.000352|
 | -0.000258  0.000352  0.996864|
Proposed new scale matrix

 |  0.017075  0.000000  0.000004|
 |  0.000000  0.011649 -0.000004|
 |  0.000002 -0.000003  0.007441|
With corresponding cell

    A    =  58.565  B   =  85.846  C    = 134.384
    Alpha=  89.960  Beta=  90.030  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  58.730  B   =  86.094  C    = 134.815
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 176.674
(Under-)estimated Z-score: 9.796

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). 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 angles: 0.559
RMS-deviation in bond angles: 1.142

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.

 124 PRO   ( 163-)  A    -2.9
 542 PRO   ( 585-)  A    -2.6
 438 TYR   ( 481-)  A    -2.4
 355 TYR   ( 394-)  A    -2.3
 474 SER   ( 517-)  A    -2.2
 303 GLU   ( 342-)  A    -2.2
 201 LEU   ( 240-)  A    -2.1
 478 ILE   ( 521-)  A    -2.1
 574 PRO   ( 617-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  84 GLU   ( 123-)  A  Poor phi/psi
 117 GLY   ( 156-)  A  Poor phi/psi
 123 GLU   ( 162-)  A  PRO omega poor
 243 THR   ( 282-)  A  omega poor
 307 ASP   ( 346-)  A  omega poor
 317 ALA   ( 356-)  A  omega poor
 321 TYR   ( 360-)  A  Poor phi/psi
 363 ARG   ( 402-)  A  Poor phi/psi
 366 ALA   ( 405-)  A  omega poor
 392 ASN   ( 431-)  A  Poor phi/psi
 511 GLN   ( 554-)  A  Poor phi/psi
 543 ASN   ( 586-)  A  omega poor
 575 GLN   ( 618-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.624

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.

   6 SER   (  45-)  A    0.37

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!

  32 THR   (  71-)  A      0
  69 GLN   ( 108-)  A      0
  84 GLU   ( 123-)  A      0
  85 ARG   ( 124-)  A      0
 114 HIS   ( 153-)  A      0
 116 ASN   ( 155-)  A      0
 118 SER   ( 157-)  A      0
 122 LEU   ( 161-)  A      0
 123 GLU   ( 162-)  A      0
 133 SER   ( 172-)  A      0
 175 VAL   ( 214-)  A      0
 220 TYR   ( 259-)  A      0
 224 HIS   ( 263-)  A      0
 234 HIS   ( 273-)  A      0
 235 LEU   ( 274-)  A      0
 240 TRP   ( 279-)  A      0
 242 GLN   ( 281-)  A      0
 244 TRP   ( 283-)  A      0
 245 SER   ( 284-)  A      0
 247 ILE   ( 286-)  A      0
 251 VAL   ( 290-)  A      0
 254 PHE   ( 293-)  A      0
 260 MET   ( 299-)  A      0
 269 GLN   ( 308-)  A      0
 271 TRP   ( 310-)  A      0
And so on for a total of 160 lines.

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].

 124 PRO   ( 163-)  A   -48.5 half-chair C-beta/C-alpha (-54 degrees)
 258 PRO   ( 297-)  A   -53.7 half-chair C-beta/C-alpha (-54 degrees)
 294 PRO   ( 333-)  A   100.7 envelop C-beta (108 degrees)
 359 PRO   ( 398-)  A  -121.2 half-chair C-delta/C-gamma (-126 degrees)
 416 PRO   ( 459-)  A  -112.8 envelop C-gamma (-108 degrees)
 457 PRO   ( 500-)  A  -128.3 half-chair C-delta/C-gamma (-126 degrees)
 472 PRO   ( 515-)  A  -116.8 envelop C-gamma (-108 degrees)
 542 PRO   ( 585-)  A   -47.8 half-chair C-beta/C-alpha (-54 degrees)
 580 PRO   ( 623-)  A   100.0 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 583 NAG   (1630-)  A      O4  <->  592 BMA   (1633-)  A      C1     0.95    1.45  INTRA B3
 583 NAG   (1630-)  A      C4  <->  592 BMA   (1633-)  A      C1     0.82    2.38  INTRA
 588  ZN   (1628-)  A     ZN   <->  589 3ES   (1635-)  A      PBY    0.44    2.86  INTRA BL
  51 ASN   (  90-)  A      ND2 <->  594 HOH   (2049 )  A      O      0.39    2.31  INTRA
 114 HIS   ( 153-)  A      CE1 <->  141 TRP   ( 180-)  A      CZ2    0.34    2.86  INTRA
 226 ASN   ( 265-)  A      ND2 <->  575 GLN   ( 618-)  A      OE1    0.29    2.41  INTRA
 114 HIS   ( 153-)  A      CE1 <->  141 TRP   ( 180-)  A      CE2    0.24    2.96  INTRA
 114 HIS   ( 153-)  A      NE2 <->  141 TRP   ( 180-)  A      CH2    0.20    2.90  INTRA
 348 HIS   ( 387-)  A      ND1 <->  371 HIS   ( 410-)  A      ND1    0.16    2.84  INTRA BL
 531 TRP   ( 574-)  A      N   <->  532 PRO   ( 575-)  A      CD     0.12    2.88  INTRA BL
 266 MET   ( 305-)  A      SD  <->  335 ASN   ( 374-)  A      C      0.12    3.28  INTRA
 574 PRO   ( 617-)  A      O   <->  576 TYR   ( 619-)  A      N      0.11    2.59  INTRA
 214 ARG   ( 253-)  A      NE  <->  569 GLU   ( 612-)  A      OE2    0.11    2.59  INTRA BL
 201 LEU   ( 240-)  A      CD2 <->  549 MET   ( 592-)  A      SD     0.11    3.29  INTRA BL
 116 ASN   ( 155-)  A      OD1 <->  117 GLY   ( 156-)  A      N      0.10    2.50  INTRA BF
 134 ARG   ( 173-)  A      NH2 <->  249 ASP   ( 288-)  A      OD1    0.09    2.61  INTRA
 314 HIS   ( 353-)  A      NE2 <->  589 3ES   (1635-)  A      OAC    0.09    2.61  INTRA BL
 121 GLN   ( 160-)  A      OE1 <->  304 LYS   ( 343-)  A      NZ     0.08    2.62  INTRA
 278 LYS   ( 317-)  A      NZ  <->  594 HOH   (2257 )  A      O      0.08    2.62  INTRA
 114 HIS   ( 153-)  A      CB  <->  115 PRO   ( 154-)  A      CD     0.07    3.03  INTRA BF
 505 HIS   ( 548-)  A      ND1 <->  594 HOH   (2380 )  A      O      0.07    2.63  INTRA
 464 ASP   ( 507-)  A      N   <->  465 PRO   ( 508-)  A      CD     0.06    2.94  INTRA BL
 114 HIS   ( 153-)  A      NE2 <->  141 TRP   ( 180-)  A      CZ2    0.06    3.04  INTRA
 427 ARG   ( 470-)  A      NH1 <->  594 HOH   (2354 )  A      O      0.05    2.65  INTRA
 147 ARG   ( 186-)  A      NH2 <->  586  CL   (1626-)  A     CL      0.05    3.05  INTRA BL
 112 VAL   ( 151-)  A      O   <->  120 LEU   ( 159-)  A      N      0.05    2.65  INTRA
 318 TRP   ( 357-)  A      N   <->  327 ARG   ( 366-)  A      O      0.05    2.65  INTRA BL
 260 MET   ( 299-)  A      CE  <->  395 SER   ( 434-)  A      N      0.04    3.06  INTRA BF
 387 HIS   ( 426-)  A      ND1 <->  594 HOH   (2328 )  A      O      0.04    2.66  INTRA
 561 ARG   ( 604-)  A      NH2 <->  594 HOH   (2404 )  A      O      0.04    2.66  INTRA
 590 3ES   (1636-)  A      NBG <->  594 HOH   (2427 )  A      O      0.04    2.66  INTRA
 242 GLN   ( 281-)  A      OE1 <->  468 LYS   ( 511-)  A      NZ     0.03    2.67  INTRA BL
 172 ASN   ( 211-)  A      ND2 <->  593 ACT   (1625-)  A      CH3    0.03    3.07  INTRA BL
  13 ASP   (  52-)  A      OD1 <->  360 VAL   ( 399-)  A      N      0.03    2.67  INTRA
 134 ARG   ( 173-)  A      NH1 <->  594 HOH   (2137 )  A      O      0.03    2.67  INTRA
 314 HIS   ( 353-)  A      O   <->  329 LYS   ( 368-)  A      NZ     0.03    2.67  INTRA BL
 529 ARG   ( 572-)  A      NH2 <->  533 GLU   ( 576-)  A      OE2    0.03    2.67  INTRA
 213 ARG   ( 252-)  A      NH2 <->  570 LYS   ( 613-)  A      O      0.03    2.67  INTRA
  61 ARG   ( 100-)  A      NH2 <->  172 ASN   ( 211-)  A      OD1    0.02    2.68  INTRA
 121 GLN   ( 160-)  A      CD  <->  304 LYS   ( 343-)  A      NZ     0.02    3.08  INTRA
 192 GLN   ( 231-)  A      NE2 <->  594 HOH   (2190 )  A      O      0.02    2.68  INTRA
 468 LYS   ( 511-)  A      NZ  <->  589 3ES   (1635-)  A      O      0.02    2.68  INTRA BL
 244 TRP   ( 283-)  A      N   <->  409 LEU   ( 452-)  A      O      0.01    2.69  INTRA BL
 217 HIS   ( 256-)  A      ND1 <->  594 HOH   (2217 )  A      O      0.01    2.69  INTRA
 312 VAL   ( 351-)  A      O   <->  329 LYS   ( 368-)  A      NZ     0.01    2.69  INTRA
 306 THR   ( 345-)  A      N   <->  307 ASP   ( 346-)  A      N      0.01    2.59  INTRA B3
 119 CYS   ( 158-)  A      SG  <->  594 HOH   (2125 )  A      O      0.01    2.99  INTRA

Packing, accessibility and threading

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.

 570 LYS   ( 613-)  A      -5.81
 223 GLN   ( 262-)  A      -5.56
 219 HIS   ( 258-)  A      -5.56
 460 GLN   ( 503-)  A      -5.56
 576 TYR   ( 619-)  A      -5.55
  67 GLN   ( 106-)  A      -5.51
 458 ARG   ( 501-)  A      -5.19
 450 GLN   ( 493-)  A      -5.13
 227 LEU   ( 266-)  A      -5.06
 500 HIS   ( 543-)  A      -5.05

Warning: Abnormal packing environment for sequential residues

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

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

 218 ARG   ( 257-)  A       220 - TYR    259- ( A)         -4.78
 297 TRP   ( 336-)  A       299 - LYS    338- ( A)         -4.18

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.

  83 LEU   ( 122-)  A   -2.99
 543 ASN   ( 586-)  A   -2.66
 184 MET   ( 223-)  A   -2.55

Water, ion, and hydrogenbond related checks

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.

 594 HOH   (2064 )  A      O     -4.66    9.13  -31.76

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.

 594 HOH   (2004 )  A      O
 594 HOH   (2034 )  A      O
 594 HOH   (2035 )  A      O
 594 HOH   (2051 )  A      O
 594 HOH   (2151 )  A      O
 594 HOH   (2165 )  A      O
 594 HOH   (2202 )  A      O
 594 HOH   (2208 )  A      O
 594 HOH   (2256 )  A      O
 594 HOH   (2430 )  A      O
Bound group on Asn; dont flip   33 ASN  (  72-) A
Bound to:  584 NAG  (1631-) A
Bound group on Asn; dont flip   70 ASN  ( 109-) A
Bound to:  582 NAG  (1629-) A
Marked this atom as acceptor  586  CL  (1626-) A     CL
Marked this atom as acceptor  587  CL  (1627-) A     CL
Metal-coordinating Histidine residue 344 fixed to   1
Metal-coordinating Histidine residue 348 fixed to   1

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.

  48 GLN   (  87-)  A
 202 GLN   ( 241-)  A
 209 HIS   ( 248-)  A
 298 ASN   ( 337-)  A
 389 HIS   ( 428-)  A
 496 GLN   ( 539-)  A

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.

  37 GLU   (  76-)  A      N
 107 TYR   ( 146-)  A      OH
 153 ALA   ( 192-)  A      N
 176 ASP   ( 215-)  A      N
 226 ASN   ( 265-)  A      ND2
 234 HIS   ( 273-)  A      NE2
 238 ASN   ( 277-)  A      N
 243 THR   ( 282-)  A      N
 272 THR   ( 311-)  A      N
 317 ALA   ( 356-)  A      N
 367 ASN   ( 406-)  A      N
 417 PHE   ( 460-)  A      N
 446 ARG   ( 489-)  A      NE
 456 VAL   ( 499-)  A      N
 477 TYR   ( 520-)  A      OH
 518 ARG   ( 561-)  A      NH1
 536 GLN   ( 579-)  A      NE2
 578 TRP   ( 621-)  A      NE1
 579 THR   ( 622-)  A      N
 581 ALA   ( 624-)  A      N
Only metal coordination for  344 HIS  ( 383-) A      NE2
Only metal coordination for  348 HIS  ( 387-) A      NE2
Only metal coordination for  372 GLU  ( 411-) A      OE1

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.

 264 GLU   ( 303-)  A      OE2
 330 GLN   ( 369-)  A      OE1
 345 GLU   ( 384-)  A      OE1
 345 GLU   ( 384-)  A      OE2

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.

 594 HOH   (2031 )  A      O  0.89  K  4
 594 HOH   (2307 )  A      O  0.94  K  4 Ion-B
 594 HOH   (2313 )  A      O  1.00  K  4
 594 HOH   (2407 )  A      O  0.98  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.

  82 ASP   ( 121-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 193 ASP   ( 232-)  A   H-bonding suggests Asn; but Alt-Rotamer
 282 ASP   ( 321-)  A   H-bonding suggests Asn
 295 GLU   ( 334-)  A   H-bonding suggests Gln; but Alt-Rotamer
 430 ASP   ( 473-)  A   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 :   0.008
  2nd generation packing quality :  -1.214
  Ramachandran plot appearance   :   0.554
  chi-1/chi-2 rotamer normality  :  -0.624
  Backbone conformation          :   0.340

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.378 (tight)
  Bond angles                    :   0.559 (tight)
  Omega angle restraints         :   0.887
  Side chain planarity           :   0.327 (tight)
  Improper dihedral distribution :   0.527
  B-factor distribution          :   0.340
  Inside/Outside distribution    :   0.995

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 : 1.97


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.378 (tight)
  Bond angles                    :   0.559 (tight)
  Omega angle restraints         :   0.887
  Side chain planarity           :   0.327 (tight)
  Improper dihedral distribution :   0.527
  B-factor distribution          :   0.340
  Inside/Outside distribution    :   0.995
==============

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