WHAT IF Check report

This file was created 2011-12-28 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 pdb1g0d.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) 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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 75101.422
Volume of the Unit Cell V= 3773658.8
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit high: Vm= 4.187
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.010

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.

 667 SO4   ( 696-)  A  -

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

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

Note: B-factor plot

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

Chain identifier: A

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.

  24 ARG   (  29-)  A
  26 ARG   (  31-)  A
  60 ARG   (  65-)  A
 212 ARG   ( 217-)  A
 230 ARG   ( 235-)  A
 243 ARG   ( 248-)  A
 260 ARG   ( 265-)  A
 310 ARG   ( 315-)  A
 319 ARG   ( 324-)  A
 336 ARG   ( 341-)  A
 405 ARG   ( 410-)  A
 453 ARG   ( 458-)  A
 505 ARG   ( 520-)  A
 510 ARG   ( 525-)  A
 545 ARG   ( 560-)  A
 641 ARG   ( 659-)  A
 651 ARG   ( 669-)  A

Warning: Tyrosine convention problem

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

 178 TYR   ( 183-)  A
 209 TYR   ( 214-)  A
 242 TYR   ( 247-)  A
 380 TYR   ( 385-)  A
 435 TYR   ( 440-)  A

Warning: Phenylalanine convention problem

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

  79 PHE   (  84-)  A
 129 PHE   ( 134-)  A
 184 PHE   ( 189-)  A
 305 PHE   ( 310-)  A
 326 PHE   ( 331-)  A
 361 PHE   ( 366-)  A
 589 PHE   ( 607-)  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.

  23 ASP   (  28-)  A
  43 ASP   (  48-)  A
 113 ASP   ( 118-)  A
 135 ASP   ( 140-)  A
 142 ASP   ( 147-)  A
 177 ASP   ( 182-)  A
 181 ASP   ( 186-)  A
 188 ASP   ( 193-)  A
 206 ASP   ( 211-)  A
 315 ASP   ( 320-)  A
 344 ASP   ( 349-)  A
 474 ASP   ( 489-)  A
 532 ASP   ( 547-)  A
 551 ASP   ( 566-)  A
 648 ASP   ( 666-)  A
 650 ASP   ( 668-)  A
 654 ASP   ( 672-)  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.

  21 GLU   (  26-)  A
  62 GLU   (  67-)  A
  87 GLU   (  92-)  A
 176 GLU   ( 181-)  A
 185 GLU   ( 190-)  A
 198 GLU   ( 203-)  A
 233 GLU   ( 238-)  A
 309 GLU   ( 314-)  A
 312 GLU   ( 317-)  A
 337 GLU   ( 342-)  A
 373 GLU   ( 378-)  A
 388 GLU   ( 393-)  A
 409 GLU   ( 414-)  A
 429 GLU   ( 434-)  A
 478 GLU   ( 493-)  A
 482 GLU   ( 497-)  A
 525 GLU   ( 540-)  A
 540 GLU   ( 555-)  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.

  17 HIS   (  22-)  A      CG   ND1  CE1 109.76    4.2
  29 VAL   (  34-)  A      N    CA   CB  101.85   -5.1
  50 HIS   (  55-)  A      CG   ND1  CE1 109.63    4.0
  71 HIS   (  76-)  A      CG   ND1  CE1 110.40    4.8
 115 HIS   ( 120-)  A      CG   ND1  CE1 109.66    4.1
 233 GLU   ( 238-)  A     -C    N    CA  130.84    5.1
 233 GLU   ( 238-)  A      N    CA   C   127.84    5.9
 237 ASP   ( 242-)  A     -C    N    CA  114.08   -4.2
 288 ILE   ( 293-)  A      CB   CG1  CD1 104.36   -4.5
 356 LEU   ( 361-)  A      N    CA   C   128.89    6.3
 357 SER   ( 362-)  A      N    CA   C    94.40   -6.0
 358 ASP   ( 363-)  A      N    CA   C   124.38    4.7
 389 VAL   ( 394-)  A      N    CA   CB  102.91   -4.5
 411 HIS   ( 416-)  A      N    CA   C    98.44   -4.6
 413 SER   ( 418-)  A      N    CA   C   123.50    4.4
 431 VAL   ( 436-)  A      N    CA   CB  103.67   -4.0
 464 HIS   ( 479-)  A      CG   ND1  CE1 109.61    4.0
 494 LEU   ( 509-)  A      CA   CB   CG  130.84    4.2
 541 HIS   ( 556-)  A      CG   ND1  CE1 109.80    4.2
 601 VAL   ( 619-)  A      C    CA   CB   98.85   -5.9
 616 HIS   ( 634-)  A      CG   ND1  CE1 109.63    4.0
 658 VAL   ( 676-)  A      N    CA   CB  117.35    4.0
 658 VAL   ( 676-)  A      C    CA   CB   99.98   -5.3
 666 LYS   ( 684-)  A     -C    N    CA  130.11    4.7

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 GLU   (  26-)  A
  23 ASP   (  28-)  A
  24 ARG   (  29-)  A
  26 ARG   (  31-)  A
  43 ASP   (  48-)  A
  60 ARG   (  65-)  A
  62 GLU   (  67-)  A
  87 GLU   (  92-)  A
 113 ASP   ( 118-)  A
 135 ASP   ( 140-)  A
 142 ASP   ( 147-)  A
 176 GLU   ( 181-)  A
 177 ASP   ( 182-)  A
 181 ASP   ( 186-)  A
 185 GLU   ( 190-)  A
 188 ASP   ( 193-)  A
 198 GLU   ( 203-)  A
 206 ASP   ( 211-)  A
 212 ARG   ( 217-)  A
 230 ARG   ( 235-)  A
 233 GLU   ( 238-)  A
 243 ARG   ( 248-)  A
 260 ARG   ( 265-)  A
 309 GLU   ( 314-)  A
 310 ARG   ( 315-)  A
And so on for a total of 52 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 356 LEU   ( 361-)  A    7.14
 357 SER   ( 362-)  A    6.56
 233 GLU   ( 238-)  A    5.59
 267 CYS   ( 272-)  A    5.33
 442 GLN   ( 447-)  A    5.04
 110 MET   ( 115-)  A    4.88
 656 LYS   ( 674-)  A    4.71
 390 ASN   ( 395-)  A    4.69
 413 SER   ( 418-)  A    4.53
 358 ASP   ( 363-)  A    4.44
 411 HIS   ( 416-)  A    4.22
 451 ALA   ( 456-)  A    4.00

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.701

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 158 TYR   ( 163-)  A      CB   4.44
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.137

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.

  47 PRO   (  52-)  A    -3.1
 665 LYS   ( 683-)  A    -2.7
 520 HIS   ( 535-)  A    -2.7
 311 LEU   ( 316-)  A    -2.7
 322 SER   ( 327-)  A    -2.7
 178 TYR   ( 183-)  A    -2.6
 550 LEU   ( 565-)  A    -2.6
 563 PRO   ( 581-)  A    -2.6
 630 LYS   ( 648-)  A    -2.5
 498 VAL   ( 513-)  A    -2.5
 624 SER   ( 642-)  A    -2.4
 164 TYR   ( 169-)  A    -2.4
 436 LYS   ( 441-)  A    -2.4
 480 LYS   ( 495-)  A    -2.4
 104 ARG   ( 109-)  A    -2.4
 513 ILE   ( 528-)  A    -2.3
 307 LEU   ( 312-)  A    -2.3
 416 LYS   ( 421-)  A    -2.3
 349 LEU   ( 354-)  A    -2.3
 482 GLU   ( 497-)  A    -2.3
 652 LEU   ( 670-)  A    -2.3
 542 HIS   ( 557-)  A    -2.3
  87 GLU   (  92-)  A    -2.2
 570 LEU   ( 588-)  A    -2.2
 592 PRO   ( 610-)  A    -2.2
And so on for a total of 64 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.

  18 ARG   (  23-)  A  Poor phi/psi
  43 ASP   (  48-)  A  Poor phi/psi
  47 PRO   (  52-)  A  Poor phi/psi
  70 GLU   (  75-)  A  Poor phi/psi
  71 HIS   (  76-)  A  Poor phi/psi
  73 ALA   (  78-)  A  Poor phi/psi
  84 ALA   (  89-)  A  Poor phi/psi
  85 GLN   (  90-)  A  Poor phi/psi
 114 GLY   ( 119-)  A  Poor phi/psi
 118 GLU   ( 123-)  A  Poor phi/psi
 141 PRO   ( 146-)  A  Poor phi/psi
 173 GLY   ( 178-)  A  Poor phi/psi
 178 TYR   ( 183-)  A  Poor phi/psi
 225 GLY   ( 230-)  A  Poor phi/psi
 233 GLU   ( 238-)  A  Poor phi/psi
 259 VAL   ( 264-)  A  Poor phi/psi
 263 LYS   ( 268-)  A  omega poor
 292 ALA   ( 297-)  A  Poor phi/psi
 294 ALA   ( 299-)  A  Poor phi/psi
 311 LEU   ( 316-)  A  Poor phi/psi
 322 SER   ( 327-)  A  Poor phi/psi
 329 TRP   ( 334-)  A  Poor phi/psi
 355 GLU   ( 360-)  A  Poor phi/psi
 364 GLY   ( 369-)  A  PRO omega poor
 379 LYS   ( 384-)  A  omega poor
 381 ASP   ( 386-)  A  Poor phi/psi
 411 HIS   ( 416-)  A  Poor phi/psi
 412 ALA   ( 417-)  A  Poor phi/psi
 413 SER   ( 418-)  A  Poor phi/psi
 502 SER   ( 517-)  A  Poor phi/psi
 505 ARG   ( 520-)  A  Poor phi/psi
 509 GLN   ( 524-)  A  Poor phi/psi
 511 LYS   ( 526-)  A  Poor phi/psi
 580 TRP   ( 598-)  A  Poor phi/psi
 624 SER   ( 642-)  A  Poor phi/psi
 654 ASP   ( 672-)  A  Poor phi/psi
 665 LYS   ( 683-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.998

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 : -4.998

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.

 498 VAL   ( 513-)  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!

   5 ASP   (  10-)  A      0
  18 ARG   (  23-)  A      0
  19 THR   (  24-)  A      0
  22 ILE   (  27-)  A      0
  23 ASP   (  28-)  A      0
  24 ARG   (  29-)  A      0
  25 GLU   (  30-)  A      0
  26 ARG   (  31-)  A      0
  31 ARG   (  36-)  A      0
  41 CYS   (  46-)  A      0
  43 ASP   (  48-)  A      0
  44 SER   (  49-)  A      0
  47 PRO   (  52-)  A      0
  48 LYS   (  53-)  A      0
  49 HIS   (  54-)  A      0
  57 LEU   (  62-)  A      0
  60 ARG   (  65-)  A      0
  62 GLU   (  67-)  A      0
  69 LYS   (  74-)  A      0
  70 GLU   (  75-)  A      0
  71 HIS   (  76-)  A      0
  73 ALA   (  78-)  A      0
  77 TRP   (  82-)  A      0
  82 GLN   (  87-)  A      0
  84 ALA   (  89-)  A      0
And so on for a total of 278 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 : 2.049

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!

 606 GLY   ( 624-)  A   1.57   12

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 177 ASP   ( 182-)  A   1.71
 232 GLU   ( 237-)  A   1.98
 296 ASP   ( 301-)  A   1.61
 380 TYR   ( 385-)  A   1.54
 412 ALA   ( 417-)  A   2.14

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]

 131 PRO   ( 136-)  A    0.15 LOW

Warning: Unusual PRO puckering phases

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

  47 PRO   (  52-)  A   160.1 half-chair C-alpha/N (162 degrees)
 141 PRO   ( 146-)  A   -57.2 half-chair C-beta/C-alpha (-54 degrees)
 261 PRO   ( 266-)  A   100.4 envelop C-beta (108 degrees)
 351 PRO   ( 356-)  A    46.9 half-chair C-delta/C-gamma (54 degrees)
 518 PRO   ( 533-)  A    51.9 half-chair C-delta/C-gamma (54 degrees)
 553 PRO   ( 568-)  A  -116.7 envelop C-gamma (-108 degrees)
 563 PRO   ( 581-)  A   -11.9 half-chair C-alpha/N (-18 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.

  70 GLU   (  75-)  A      O   <->   72 GLY   (  77-)  A      N      0.46    2.24  INTRA BF
 412 ALA   ( 417-)  A      O   <->  416 LYS   ( 421-)  A      NZ     0.46    2.24  INTRA BF
  30 ARG   (  35-)  A      NH2 <->  668 HOH   ( 876 )  A      O      0.42    2.28  INTRA BL
  52 GLU   (  57-)  A      OE2 <->   69 LYS   (  74-)  A      NZ     0.40    2.30  INTRA BF
 547 LYS   ( 562-)  A      NZ  <->  668 HOH   ( 712 )  A      O      0.31    2.39  INTRA BL
  68 GLN   (  73-)  A      NE2 <->   72 GLY   (  77-)  A      CA     0.30    2.80  INTRA BF
 293 SER   ( 298-)  A      OG  <->  388 GLU   ( 393-)  A      OE2    0.30    2.10  INTRA BL
  43 ASP   (  48-)  A      CG  <->   44 SER   (  49-)  A      N      0.29    2.71  INTRA BF
 523 HIS   ( 538-)  A      NE2 <->  525 GLU   ( 540-)  A      CG     0.27    2.83  INTRA BF
 257 ALA   ( 262-)  A      O   <->  260 ARG   ( 265-)  A      NH1    0.25    2.45  INTRA BF
 132 TRP   ( 137-)  A      CH2 <->  151 MET   ( 156-)  A      CE     0.23    2.97  INTRA BL
   2 LEU   (   7-)  A      CD1 <->    3 ILE   (   8-)  A      N      0.23    2.77  INTRA BF
 531 TYR   ( 546-)  A      O   <->  535 VAL   ( 550-)  A      CG2    0.23    2.57  INTRA
 267 CYS   ( 272-)  A      SG  <->  500 TYR   ( 515-)  A      OH     0.22    2.78  INTRA BL
 233 GLU   ( 238-)  A      O   <->  235 TYR   ( 240-)  A      N      0.21    2.49  INTRA
   2 LEU   (   7-)  A      CD1 <->    3 ILE   (   8-)  A      CG1    0.21    2.99  INTRA BF
  26 ARG   (  31-)  A      NH2 <->  181 ASP   ( 186-)  A      OD1    0.20    2.50  INTRA BL
  70 GLU   (  75-)  A      O   <->   71 HIS   (  76-)  A      C      0.20    2.40  INTRA BF
 188 ASP   ( 193-)  A      OD1 <->  204 ARG   ( 209-)  A      NH2    0.19    2.51  INTRA BL
  52 GLU   (  57-)  A      CD  <->   69 LYS   (  74-)  A      NZ     0.18    2.92  INTRA BF
  55 LEU   (  60-)  A      N   <->   65 ILE   (  70-)  A      O      0.17    2.53  INTRA
 607 ALA   ( 625-)  A      N   <->  668 HOH   ( 894 )  A      O      0.17    2.53  INTRA BL
 411 HIS   ( 416-)  A      N   <->  412 ALA   ( 417-)  A      N      0.16    2.44  INTRA BF
  46 PRO   (  51-)  A      O   <->   49 HIS   (  54-)  A      N      0.16    2.54  INTRA BF
 464 HIS   ( 479-)  A      CD2 <->  466 GLN   ( 481-)  A      N      0.16    2.94  INTRA
And so on for a total of 170 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

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.

 424 TYR   ( 429-)  A      -7.82
  60 ARG   (  65-)  A      -6.27
  71 HIS   (  76-)  A      -6.08
 380 TYR   ( 385-)  A      -6.03
 485 ARG   ( 500-)  A      -5.96
 400 LYS   ( 405-)  A      -5.76
  74 ARG   (  79-)  A      -5.59
 504 ARG   ( 519-)  A      -5.57
 310 ARG   ( 315-)  A      -5.55
  85 GLN   (  90-)  A      -5.49
 379 LYS   ( 384-)  A      -5.47
 618 ASN   ( 636-)  A      -5.42
 665 LYS   ( 683-)  A      -5.39
 243 ARG   ( 248-)  A      -5.38
 134 ARG   ( 139-)  A      -5.34
 341 GLU   ( 346-)  A      -5.27
 637 ARG   ( 655-)  A      -5.25
 434 HIS   ( 439-)  A      -5.25

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

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.

 501 ASN   ( 516-)  A   -3.39
 541 HIS   ( 556-)  A   -2.65

Warning: Abnormal packing Z-score for sequential residues

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

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

 408 THR   ( 413-)  A     -  411 HIS   ( 416-)  A        -1.82
 514 SER   ( 529-)  A     -  517 VAL   ( 532-)  A        -2.03

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

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.

 668 HOH   ( 776 )  A      O     59.54    3.55   -9.26
 668 HOH   ( 945 )  A      O     41.49   46.56    8.88
 668 HOH   ( 986 )  A      O     37.34   50.28   12.84
 668 HOH   (1023 )  A      O     51.33   35.94   24.57
 668 HOH   (1069 )  A      O     48.73   -4.26    4.39
 668 HOH   (1073 )  A      O     42.90   42.52   10.39

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.

 668 HOH   ( 773 )  A      O
 668 HOH   ( 915 )  A      O
 668 HOH   ( 978 )  A      O
 668 HOH   (1003 )  A      O
 668 HOH   (1004 )  A      O
 668 HOH   (1005 )  A      O
 668 HOH   (1018 )  A      O
 668 HOH   (1024 )  A      O
 668 HOH   (1035 )  A      O
 668 HOH   (1043 )  A      O

Error: HIS, ASN, GLN side chain flips

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

 253 GLN   ( 258-)  A
 327 HIS   ( 332-)  A
 426 ASN   ( 431-)  A
 464 HIS   ( 479-)  A
 501 ASN   ( 516-)  A
 542 HIS   ( 557-)  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.

   9 ARG   (  14-)  A      NH1
  26 ARG   (  31-)  A      N
  43 ASP   (  48-)  A      N
  44 SER   (  49-)  A      N
  59 LYS   (  64-)  A      N
  68 GLN   (  73-)  A      NE2
  76 LYS   (  81-)  A      N
  85 GLN   (  90-)  A      N
  87 GLU   (  92-)  A      N
  94 SER   (  99-)  A      N
 205 SER   ( 210-)  A      N
 209 TYR   ( 214-)  A      N
 219 ASN   ( 224-)  A      N
 220 SER   ( 225-)  A      N
 248 VAL   ( 253-)  A      N
 266 GLN   ( 271-)  A      N
 286 ARG   ( 291-)  A      NH1
 286 ARG   ( 291-)  A      NH2
 291 PHE   ( 296-)  A      N
 297 VAL   ( 302-)  A      N
 317 ARG   ( 322-)  A      NE
 326 PHE   ( 331-)  A      N
 346 TRP   ( 351-)  A      NE1
 352 THR   ( 357-)  A      OG1
 355 GLU   ( 360-)  A      N
 378 VAL   ( 383-)  A      N
 382 ALA   ( 387-)  A      N
 389 VAL   ( 394-)  A      N
 412 ALA   ( 417-)  A      N
 417 ASN   ( 422-)  A      N
 427 HIS   ( 432-)  A      N
 428 ARG   ( 433-)  A      NH1
 506 GLY   ( 521-)  A      N
 523 HIS   ( 538-)  A      NE2
 531 TYR   ( 546-)  A      OH
 532 ASP   ( 547-)  A      N
 539 SER   ( 554-)  A      N
 541 HIS   ( 556-)  A      N
 541 HIS   ( 556-)  A      NE2
 543 LEU   ( 558-)  A      N
 559 VAL   ( 577-)  A      N
 561 ASN   ( 579-)  A      ND2
 575 GLY   ( 593-)  A      N
 595 VAL   ( 613-)  A      N
 654 ASP   ( 672-)  A      N
 665 LYS   ( 683-)  A      N
 666 LYS   ( 684-)  A      N

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.

  49 HIS   (  54-)  A      ND1
 290 ASN   ( 295-)  A      OD1
 434 HIS   ( 439-)  A      NE2
 541 HIS   ( 556-)  A      ND1
 664 HIS   ( 682-)  A      ND1

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.

 198 GLU   ( 203-)  A   H-bonding suggests Gln
 446 GLU   ( 451-)  A   H-bonding suggests Gln; but Alt-Rotamer
 507 GLU   ( 522-)  A   H-bonding suggests Gln

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 :  -0.539
  2nd generation packing quality :  -2.094
  Ramachandran plot appearance   :  -2.137
  chi-1/chi-2 rotamer normality  :  -4.998 (bad)
  Backbone conformation          :  -0.375

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.653 (tight)
  Bond angles                    :   0.944
  Omega angle restraints         :   0.373 (tight)
  Side chain planarity           :   0.293 (tight)
  Improper dihedral distribution :   0.858
  B-factor distribution          :   1.116
  Inside/Outside distribution    :   1.002

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -2.9
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.653 (tight)
  Bond angles                    :   0.944
  Omega angle restraints         :   0.373 (tight)
  Side chain planarity           :   0.293 (tight)
  Improper dihedral distribution :   0.858
  B-factor distribution          :   1.116
  Inside/Outside distribution    :   1.002
==============

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.