WHAT IF Check report

This file was created 2011-12-15 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 pdb1ebv.ent

Checks that need to be done early-on in validation

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 63525.680
Volume of the Unit Cell V= 4553394.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 8.960
Vm by authors and this calculated Vm do not agree very well

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.

 558 SCL   ( 700-)  A  -

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.

 553 NAG   ( 671-)  A  -   O4  bound to  554 NAG   ( 672-)  A  -   C1

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:

Crystal temperature (K) :100.000

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

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

Percentage of buried atoms with B less than 5 : 32.09

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.

 148 ARG   ( 180-)  A
 427 ARG   ( 459-)  A

Warning: Tyrosine convention problem

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

  98 TYR   ( 130-)  A
 210 TYR   ( 242-)  A
 316 TYR   ( 348-)  A
 323 TYR   ( 355-)  A
 341 TYR   ( 373-)  A
 353 TYR   ( 385-)  A
 372 TYR   ( 404-)  A
 443 TYR   ( 475-)  A
 463 TYR   ( 495-)  A
 512 TYR   ( 544-)  A

Warning: Phenylalanine convention problem

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

  18 PHE   (  50-)  A
  56 PHE   (  88-)  A
  70 PHE   ( 102-)  A
 149 PHE   ( 181-)  A
 166 PHE   ( 198-)  A
 169 PHE   ( 201-)  A
 177 PHE   ( 209-)  A
 188 PHE   ( 220-)  A
 335 PHE   ( 367-)  A
 486 PHE   ( 518-)  A
 497 PHE   ( 529-)  A
 518 PHE   ( 550-)  A
 548 PHE   ( 580-)  A

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.

  21 ASP   (  53-)  A
 282 ASP   ( 314-)  A
 361 ASP   ( 393-)  A
 369 ASP   ( 401-)  A
 465 ASP   ( 497-)  A

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.

  41 GLU   (  73-)  A
 143 GLU   ( 175-)  A
 236 GLU   ( 268-)  A
 276 GLU   ( 308-)  A
 287 GLU   ( 319-)  A
 307 GLU   ( 339-)  A
 332 GLU   ( 364-)  A
 373 GLU   ( 405-)  A
 448 GLU   ( 480-)  A
 461 GLU   ( 493-)  A
 478 GLU   ( 510-)  A
 521 GLU   ( 553-)  A

Geometric checks

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

 116 TYR   ( 148-)  A      N    CA   C    99.23   -4.3

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.

  21 ASP   (  53-)  A
  41 GLU   (  73-)  A
 143 GLU   ( 175-)  A
 148 ARG   ( 180-)  A
 236 GLU   ( 268-)  A
 276 GLU   ( 308-)  A
 282 ASP   ( 314-)  A
 287 GLU   ( 319-)  A
 307 GLU   ( 339-)  A
 332 GLU   ( 364-)  A
 361 ASP   ( 393-)  A
 369 ASP   ( 401-)  A
 373 GLU   ( 405-)  A
 427 ARG   ( 459-)  A
 448 GLU   ( 480-)  A
 461 GLU   ( 493-)  A
 465 ASP   ( 497-)  A
 478 GLU   ( 510-)  A
 521 GLU   ( 553-)  A

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.

 314 GLU   ( 346-)  A    5.92
 476 LEU   ( 508-)  A    4.93
 448 GLU   ( 480-)  A    4.83
 116 TYR   ( 148-)  A    4.57
 537 CYS   ( 569-)  A    4.49
  98 TYR   ( 130-)  A    4.29
 376 LEU   ( 408-)  A    4.27
 260 PHE   ( 292-)  A    4.23
 149 PHE   ( 181-)  A    4.13

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 : -3.788

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.

 486 PHE   ( 518-)  A    -3.4
 482 PRO   ( 514-)  A    -3.0
  42 ILE   (  74-)  A    -2.7
 544 PRO   ( 576-)  A    -2.5
 353 TYR   ( 385-)  A    -2.5
 466 ILE   ( 498-)  A    -2.5
   7 TYR   (  39-)  A    -2.4
 375 PHE   ( 407-)  A    -2.4
 206 LEU   ( 238-)  A    -2.3
  29 ARG   (  61-)  A    -2.3
 452 GLU   ( 484-)  A    -2.3
  37 CYS   (  69-)  A    -2.3
 275 ARG   ( 307-)  A    -2.3
 294 GLU   ( 326-)  A    -2.2
  17 ARG   (  49-)  A    -2.2
  33 SER   (  65-)  A    -2.2
 483 ASN   ( 515-)  A    -2.2
 379 THR   ( 411-)  A    -2.2
  50 LEU   (  82-)  A    -2.1
 426 LEU   ( 458-)  A    -2.1
  98 TYR   ( 130-)  A    -2.1
 100 ILE   ( 132-)  A    -2.1
 118 ARG   ( 150-)  A    -2.1
 444 THR   ( 476-)  A    -2.1
 531 THR   ( 563-)  A    -2.1
 344 ARG   ( 376-)  A    -2.1
 198 LEU   ( 230-)  A    -2.1
 290 THR   ( 322-)  A    -2.1
  22 ARG   (  54-)  A    -2.0
 117 THR   ( 149-)  A    -2.0
  65 ARG   (  97-)  A    -2.0
 132 GLY   ( 164-)  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.

  12 GLN   (  44-)  A  Poor phi/psi
  74 THR   ( 106-)  A  Poor phi/psi
  94 SER   ( 126-)  A  PRO omega poor
  97 THR   ( 129-)  A  Poor phi/psi
 133 THR   ( 165-)  A  Poor phi/psi
 194 HIS   ( 226-)  A  Poor phi/psi
 198 LEU   ( 230-)  A  Poor phi/psi
 215 PHE   ( 247-)  A  Poor phi/psi
 217 ASP   ( 249-)  A  Poor phi/psi
 238 PRO   ( 270-)  A  Poor phi/psi
 255 VAL   ( 287-)  A  Poor phi/psi
 263 LEU   ( 295-)  A  Poor phi/psi
 341 TYR   ( 373-)  A  Poor phi/psi
 376 LEU   ( 408-)  A  Poor phi/psi
 380 SER   ( 412-)  A  Poor phi/psi
 452 GLU   ( 484-)  A  Poor phi/psi
 513 TRP   ( 545-)  A  Poor phi/psi
 547 SER   ( 579-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.489

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.489

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.

 109 SER   ( 141-)  A    0.36
 146 SER   ( 178-)  A    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!

   4 CYS   (  36-)  A      0
   5 CYS   (  37-)  A      0
   7 TYR   (  39-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  11 HIS   (  43-)  A      0
  12 GLN   (  44-)  A      0
  20 LEU   (  52-)  A      0
  21 ASP   (  53-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 TYR   (  64-)  A      0
  33 SER   (  65-)  A      0
  35 PRO   (  67-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  42 ILE   (  74-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  73 ALA   ( 105-)  A      0
  91 LEU   ( 123-)  A      0
  93 PRO   ( 125-)  A      0
And so on for a total of 205 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 : 1.160

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]

  40 PRO   (  72-)  A    0.46 HIGH

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.

 447 GLN   ( 479-)  A      CB  <->  453 LYS   ( 485-)  A      NZ     0.26    2.84  INTRA
 229 VAL   ( 261-)  A      O   <->  275 ARG   ( 307-)  A      NH1    0.26    2.44  INTRA BL
 153 ARG   ( 185-)  A      NH2 <->  406 ARG   ( 438-)  A      NH1    0.26    2.59  INTRA
 163 ASN   ( 195-)  A      ND2 <->  548 PHE   ( 580-)  A      C      0.25    2.85  INTRA BL
 549 HIS   ( 581-)  A      ND1 <->  550 VAL   ( 582-)  A      O      0.24    2.36  INTRA
 512 TYR   ( 544-)  A      O   <->  514 LYS   ( 546-)  A      N      0.24    2.46  INTRA BL
  88 ARG   ( 120-)  A      NH2 <->  492 GLU   ( 524-)  A      OE1    0.24    2.46  INTRA BL
 356 HIS   ( 388-)  A      N   <->  357 PRO   ( 389-)  A      CD     0.23    2.77  INTRA BL
 148 ARG   ( 180-)  A      O   <->  406 ARG   ( 438-)  A      NH1    0.22    2.48  INTRA
  89 SER   ( 121-)  A      O   <->   91 LEU   ( 123-)  A      N      0.22    2.48  INTRA BL
  91 LEU   ( 123-)  A      O   <->  437 ARG   ( 469-)  A      NH2    0.21    2.49  INTRA BL
 237 ALA   ( 269-)  A      O   <->  239 VAL   ( 271-)  A      N      0.20    2.50  INTRA
 432 ASN   ( 464-)  A      OD1 <->  443 TYR   ( 475-)  A      N      0.20    2.50  INTRA BL
 465 ASP   ( 497-)  A      O   <->  468 ALA   ( 500-)  A      N      0.19    2.51  INTRA BL
 355 TRP   ( 387-)  A      C   <->  357 PRO   ( 389-)  A      CD     0.18    3.02  INTRA BL
 209 GLN   ( 241-)  A      NE2 <->  213 ARG   ( 245-)  A      NH1    0.18    2.67  INTRA BL
  88 ARG   ( 120-)  A      NH2 <->  492 GLU   ( 524-)  A      CD     0.18    2.92  INTRA BL
 225 LEU   ( 257-)  A      O   <->  228 GLU   ( 260-)  A      N      0.16    2.54  INTRA
 114 SER   ( 146-)  A      N   <->  115 TYR   ( 147-)  A      N      0.16    2.44  INTRA BL
  64 GLY   (  96-)  A      O   <->   67 LEU   (  99-)  A      N      0.16    2.54  INTRA
 202 TYR   ( 234-)  A      OH  <->  277 HIS   ( 309-)  A      ND1    0.15    2.55  INTRA BL
 356 HIS   ( 388-)  A      NE2 <->  557 HEM   ( 601-)  A      NC     0.15    2.85  INTRA BL
 481 HIS   ( 513-)  A      CB  <->  482 PRO   ( 514-)  A      CD     0.14    2.96  INTRA
 452 GLU   ( 484-)  A      OE2 <->  455 MET   ( 487-)  A      N      0.14    2.56  INTRA
 498 OAS   ( 530-)  A      OAC <->  558 SCL   ( 700-)  A      C5     0.14    2.66  INTRA
And so on for a total of 131 lines.

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.

 245 ARG   ( 277-)  A      -8.00
  29 ARG   (  61-)  A      -7.22
 338 GLN   ( 370-)  A      -6.74
 138 GLN   ( 170-)  A      -6.68
  20 LEU   (  52-)  A      -6.14
 342 ARG   ( 374-)  A      -6.10
 153 ARG   ( 185-)  A      -6.02
 183 LYS   ( 215-)  A      -5.90
  17 ARG   (  49-)  A      -5.90
 411 HIS   ( 443-)  A      -5.56
  51 ARG   (  83-)  A      -5.36
 396 ARG   ( 428-)  A      -5.32
 148 ARG   ( 180-)  A      -5.26
 137 LYS   ( 169-)  A      -5.20
 155 PHE   ( 187-)  A      -5.18
 437 ARG   ( 469-)  A      -5.08
 104 TYR   ( 136-)  A      -5.07
  22 ARG   (  54-)  A      -5.02

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.

 137 LYS   ( 169-)  A       139 - LEU    171- ( A)         -5.60
 152 ARG   ( 184-)  A       155 - PHE    187- ( A)         -4.82

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  10 GLN   (  42-)  A
  63 HIS   (  95-)  A
 176 GLN   ( 208-)  A
 205 ASN   ( 237-)  A
 209 GLN   ( 241-)  A
 288 HIS   ( 320-)  A
 411 HIS   ( 443-)  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.

  36 ASN   (  68-)  A      N
  43 TRP   (  75-)  A      N
  51 ARG   (  83-)  A      N
  73 ALA   ( 105-)  A      N
  77 ARG   ( 109-)  A      N
 100 ILE   ( 132-)  A      N
 106 SER   ( 138-)  A      N
 106 SER   ( 138-)  A      OG
 118 ARG   ( 150-)  A      NE
 118 ARG   ( 150-)  A      NH1
 118 ARG   ( 150-)  A      NH2
 119 ILE   ( 151-)  A      N
 171 GLN   ( 203-)  A      NE2
 172 HIS   ( 204-)  A      NE2
 176 GLN   ( 208-)  A      NE2
 181 SER   ( 213-)  A      OG
 192 LEU   ( 224-)  A      N
 199 GLY   ( 231-)  A      N
 204 ASP   ( 236-)  A      N
 207 GLU   ( 239-)  A      N
 208 ARG   ( 240-)  A      NH2
 215 PHE   ( 247-)  A      N
 216 LYS   ( 248-)  A      N
 229 VAL   ( 261-)  A      N
 255 VAL   ( 287-)  A      N
And so on for a total of 58 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.

 172 HIS   ( 204-)  A      ND1
 351 GLN   ( 383-)  A      OE1
 369 ASP   ( 401-)  A      OD1

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.

 197 ASP   ( 229-)  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 :  -2.011
  2nd generation packing quality :  -1.837
  Ramachandran plot appearance   :  -3.788 (poor)
  chi-1/chi-2 rotamer normality  :  -3.489 (poor)
  Backbone conformation          :  -0.759

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.664 (tight)
  Omega angle restraints         :   0.211 (tight)
  Side chain planarity           :   0.215 (tight)
  Improper dihedral distribution :   0.641
  Inside/Outside distribution    :   1.100

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 : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.664 (tight)
  Omega angle restraints         :   0.211 (tight)
  Side chain planarity           :   0.215 (tight)
  Improper dihedral distribution :   0.641
  Inside/Outside distribution    :   1.100
==============

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.