WHAT IF Check report

This file was created 2013-12-09 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 pdb3qju.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.

 756 HAS   ( 801-)  A  -         Atom types
 757 CUA   ( 802-)  B  -         Atom types
 758 CMO   ( 563-)  A  -         Size
 759 HEM   ( 800-)  A  -         OK

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   3 GLU   (  13-)  A    High
  47 ARG   (  57-)  A    High
 317 ARG   ( 327-)  A    High
 318 GLY   ( 328-)  A    High
 319 GLY   ( 329-)  A    High
 320 ARG   ( 330-)  A    High
 321 GLY   ( 331-)  A    High
 322 LEU   ( 332-)  A    High
 324 GLY   ( 334-)  A    High
 327 ARG   ( 337-)  A    High
 402 PRO   ( 412-)  A    High
 404 SER   ( 414-)  A    High
 405 ASP   ( 415-)  A    High
 406 ALA   ( 416-)  A    High
 407 GLN   ( 417-)  A    High
 408 ARG   ( 418-)  A    High
 409 ARG   ( 419-)  A    High
 476 TYR   ( 486-)  A    High
 483 LEU   ( 493-)  A    High
 484 SER   ( 494-)  A    High
 485 ARG   ( 495-)  A    High
 486 GLU   ( 496-)  A    High
 487 ARG   ( 497-)  A    High
 488 LYS   ( 498-)  A    High
 489 PRO   ( 499-)  A    High
 490 GLU   ( 500-)  A    High
 553 ASP   (   3-)  B    High
 554 GLU   (   4-)  B    High
 555 HIS   (   5-)  B    High
 556 LYS   (   6-)  B    High
 557 ALA   (   7-)  B    High
 558 HIS   (   8-)  B    High
 559 LYS   (   9-)  B    High
 560 ALA   (  10-)  B    High
 561 ILE   (  11-)  B    High
 562 LEU   (  12-)  B    High
 563 ALA   (  13-)  B    High
 564 TYR   (  14-)  B    High
 718 GLU   ( 168-)  B    High

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: 3

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

  47 ARG   (  57-)  A
  85 ARG   (  95-)  A
  90 ARG   ( 100-)  A
 158 ARG   ( 168-)  A
 159 ARG   ( 169-)  A
 215 ARG   ( 225-)  A
 315 ARG   ( 325-)  A
 317 ARG   ( 327-)  A
 320 ARG   ( 330-)  A
 408 ARG   ( 418-)  A
 439 ARG   ( 449-)  A
 440 ARG   ( 450-)  A
 485 ARG   ( 495-)  A
 508 ARG   ( 518-)  A
 516 ARG   ( 526-)  A
 550 ARG   ( 560-)  A
 602 ARG   (  52-)  B
 609 ARG   (  59-)  B
 686 ARG   ( 136-)  B
 691 ARG   ( 141-)  B
 696 ARG   ( 146-)  B
 750 ARG   (  33-)  C

Warning: Tyrosine convention problem

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

  13 TYR   (  23-)  A
  56 TYR   (  66-)  A
 126 TYR   ( 136-)  A
 136 TYR   ( 146-)  A
 234 TYR   ( 244-)  A
 238 TYR   ( 248-)  A
 363 TYR   ( 373-)  A
 442 TYR   ( 452-)  A
 450 TYR   ( 460-)  A
 476 TYR   ( 486-)  A
 640 TYR   (  90-)  B
 687 TYR   ( 137-)  B

Warning: Phenylalanine convention problem

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

  19 PHE   (  29-)  A
  28 PHE   (  38-)  A
  51 PHE   (  61-)  A
 104 PHE   ( 114-)  A
 125 PHE   ( 135-)  A
 184 PHE   ( 194-)  A
 203 PHE   ( 213-)  A
 218 PHE   ( 228-)  A
 228 PHE   ( 238-)  A
 262 PHE   ( 272-)  A
 271 PHE   ( 281-)  A
 275 PHE   ( 285-)  A
 294 PHE   ( 304-)  A
 304 PHE   ( 314-)  A
 359 PHE   ( 369-)  A
 419 PHE   ( 429-)  A
 474 PHE   ( 484-)  A
 479 PHE   ( 489-)  A
 498 PHE   ( 508-)  A
 521 PHE   ( 531-)  A
 540 PHE   ( 550-)  A
 571 PHE   (  21-)  B
 579 PHE   (  29-)  B
 638 PHE   (  88-)  B
 711 PHE   ( 161-)  B

Warning: Aspartic acid convention problem

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

  40 ASP   (  50-)  A
 155 ASP   ( 165-)  A
 252 ASP   ( 262-)  A
 277 ASP   ( 287-)  A
 362 ASP   ( 372-)  A
 405 ASP   ( 415-)  A
 507 ASP   ( 517-)  A
 515 ASP   ( 525-)  A
 661 ASP   ( 111-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  86 GLU   (  96-)  A
 118 GLU   ( 128-)  A
 193 GLU   ( 203-)  A
 207 GLU   ( 217-)  A
 311 GLU   ( 321-)  A
 500 GLU   ( 510-)  A
 506 GLU   ( 516-)  A
 554 GLU   (   4-)  B
 565 GLU   (  15-)  B
 601 GLU   (  51-)  B
 669 GLU   ( 119-)  B

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 178 VAL   ( 188-)  A      CA   CB    1.63    4.9
 364 VAL   ( 374-)  A      CA   CB    1.61    4.1

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998282  0.000197  0.000249|
 |  0.000197  0.997786 -0.000306|
 |  0.000249 -0.000306  0.995011|
Proposed new scale matrix

 |  0.009128 -0.000002 -0.000002|
 | -0.000002  0.009132  0.000003|
 | -0.000002  0.000002  0.006099|
With corresponding cell

    A    = 109.557  B   = 109.502  C    = 163.950
    Alpha=  90.035  Beta=  89.971  Gamma=  89.977

The CRYST1 cell dimensions

    A    = 109.750  B   = 109.750  C    = 164.770
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 242.223
(Under-)estimated Z-score: 11.470

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.

 220 TRP   ( 230-)  A      C    CA   CB  118.66    4.5
 223 HIS   ( 233-)  A      N    CA   CB  117.57    4.2
 223 HIS   ( 233-)  A      CA   CB   CG  109.76   -4.0
 374 HIS   ( 384-)  A      CG   ND1  CE1 109.62    4.0

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.

  40 ASP   (  50-)  A
  47 ARG   (  57-)  A
  85 ARG   (  95-)  A
  86 GLU   (  96-)  A
  90 ARG   ( 100-)  A
 118 GLU   ( 128-)  A
 155 ASP   ( 165-)  A
 158 ARG   ( 168-)  A
 159 ARG   ( 169-)  A
 193 GLU   ( 203-)  A
 207 GLU   ( 217-)  A
 215 ARG   ( 225-)  A
 252 ASP   ( 262-)  A
 277 ASP   ( 287-)  A
 311 GLU   ( 321-)  A
 315 ARG   ( 325-)  A
 317 ARG   ( 327-)  A
 320 ARG   ( 330-)  A
 362 ASP   ( 372-)  A
 405 ASP   ( 415-)  A
 408 ARG   ( 418-)  A
 439 ARG   ( 449-)  A
 440 ARG   ( 450-)  A
 485 ARG   ( 495-)  A
 500 GLU   ( 510-)  A
 506 GLU   ( 516-)  A
 507 ASP   ( 517-)  A
 508 ARG   ( 518-)  A
 515 ASP   ( 525-)  A
 516 ARG   ( 526-)  A
 550 ARG   ( 560-)  A
 554 GLU   (   4-)  B
 565 GLU   (  15-)  B
 601 GLU   (  51-)  B
 602 ARG   (  52-)  B
 609 ARG   (  59-)  B
 661 ASP   ( 111-)  B
 669 GLU   ( 119-)  B
 686 ARG   ( 136-)  B
 691 ARG   ( 141-)  B
 696 ARG   ( 146-)  B
 750 ARG   (  33-)  C

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.

 355 VAL   ( 365-)  A    4.85
 171 LEU   ( 181-)  A    4.77
 365 VAL   ( 375-)  A    4.56
 270 GLY   ( 280-)  A    4.36
 455 VAL   ( 465-)  A    4.24

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 223 HIS   ( 233-)  A    4.71

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.029

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.

 359 PHE   ( 369-)  A    -3.6
 638 PHE   (  88-)  B    -3.1
 658 THR   ( 108-)  B    -3.0
 508 ARG   ( 518-)  A    -2.9
 660 PRO   ( 110-)  B    -2.8
 713 THR   ( 163-)  B    -2.6
 374 HIS   ( 384-)  A    -2.6
 268 PRO   ( 278-)  A    -2.5
 442 TYR   ( 452-)  A    -2.5
 125 PHE   ( 135-)  A    -2.4
 439 ARG   ( 449-)  A    -2.4
 497 PRO   ( 507-)  A    -2.3
 373 GLY   ( 383-)  A    -2.3
 720 GLU   (   3-)  C    -2.3
 428 GLY   ( 438-)  A    -2.3
 491 LEU   ( 501-)  A    -2.2
 360 THR   ( 370-)  A    -2.2
 368 THR   ( 378-)  A    -2.2
 145 SER   ( 155-)  A    -2.2
 661 ASP   ( 111-)  B    -2.2
  38 ASN   (  48-)  A    -2.1
 662 VAL   ( 112-)  B    -2.1
 716 VAL   ( 166-)  B    -2.1
 554 GLU   (   4-)  B    -2.1
   5 TYR   (  15-)  A    -2.1
 559 LYS   (   9-)  B    -2.0
 206 VAL   ( 216-)  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.

   3 GLU   (  13-)  A  omega poor
   4 ALA   (  14-)  A  omega poor
  38 ASN   (  48-)  A  Poor phi/psi
  77 ALA   (  87-)  A  omega poor
 117 ASN   ( 127-)  A  Poor phi/psi
 120 THR   ( 130-)  A  omega poor
 122 LEU   ( 132-)  A  Poor phi/psi
 125 PHE   ( 135-)  A  Poor phi/psi
 127 PRO   ( 137-)  A  PRO omega poor
 166 GLY   ( 176-)  A  Poor phi/psi
 186 ALA   ( 196-)  A  omega poor
 222 GLY   ( 232-)  A  omega poor
 248 LYS   ( 258-)  A  omega poor
 319 GLY   ( 329-)  A  omega poor
 320 ARG   ( 330-)  A  Poor phi/psi, omega poor
 324 GLY   ( 334-)  A  Poor phi/psi
 332 ASP   ( 342-)  A  omega poor
 351 ALA   ( 361-)  A  omega poor
 357 ALA   ( 367-)  A  omega poor
 358 SER   ( 368-)  A  Poor phi/psi
 359 PHE   ( 369-)  A  Poor phi/psi
 373 GLY   ( 383-)  A  Poor phi/psi
 374 HIS   ( 384-)  A  Poor phi/psi, omega poor
 381 SER   ( 391-)  A  Poor phi/psi
 428 GLY   ( 438-)  A  Poor phi/psi
 435 LEU   ( 445-)  A  omega poor
 436 ASN   ( 446-)  A  Poor phi/psi
 440 ARG   ( 450-)  A  Poor phi/psi
 445 GLN   ( 455-)  A  omega poor
 508 ARG   ( 518-)  A  Poor phi/psi
 516 ARG   ( 526-)  A  Poor phi/psi
 554 GLU   (   4-)  B  Poor phi/psi
 607 THR   (  57-)  B  Poor phi/psi
 609 ARG   (  59-)  B  omega poor
 610 GLN   (  60-)  B  Poor phi/psi
 619 GLN   (  69-)  B  omega poor
 637 ALA   (  87-)  B  omega poor
 638 PHE   (  88-)  B  Poor phi/psi
 641 GLN   (  91-)  B  PRO omega poor
 643 ASN   (  93-)  B  PRO omega poor
 650 GLY   ( 100-)  B  Poor phi/psi
 661 ASP   ( 111-)  B  Poor phi/psi
 722 PRO   (   5-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.847

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 : -3.847

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.

 309 SER   ( 319-)  A    0.36
 140 SER   ( 150-)  A    0.37
 299 SER   ( 309-)  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 ALA   (  14-)  A      0
   5 TYR   (  15-)  A      0
  38 ASN   (  48-)  A      0
  41 ALA   (  51-)  A      0
  49 LEU   (  59-)  A      0
  53 GLN   (  63-)  A      0
  89 MET   (  99-)  A      0
  92 ASN   ( 102-)  A      0
  93 MET   ( 103-)  A      0
 117 ASN   ( 127-)  A      0
 119 ALA   ( 129-)  A      0
 120 THR   ( 130-)  A      0
 121 VAL   ( 131-)  A      0
 122 LEU   ( 132-)  A      0
 125 PHE   ( 135-)  A      0
 126 TYR   ( 136-)  A      0
 127 PRO   ( 137-)  A      0
 128 PRO   ( 138-)  A      0
 129 LEU   ( 139-)  A      0
 132 HIS   ( 142-)  A      0
 165 PRO   ( 175-)  A      0
 198 LEU   ( 208-)  A      0
 203 PHE   ( 213-)  A      0
 205 LEU   ( 215-)  A      0
 219 TRP   ( 229-)  A      0
And so on for a total of 195 lines.

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]

  43 PRO   (  53-)  A    0.09 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].

  30 PRO   (  40-)  A   105.3 envelop C-beta (108 degrees)
 113 PRO   ( 123-)  A   107.5 envelop C-beta (108 degrees)
 200 PRO   ( 210-)  A  -172.7 envelop N (180 degrees)
 268 PRO   ( 278-)  A   -53.5 half-chair C-beta/C-alpha (-54 degrees)
 282 PRO   ( 292-)  A   131.7 half-chair C-beta/C-alpha (126 degrees)
 298 PRO   ( 308-)  A   127.8 half-chair C-beta/C-alpha (126 degrees)
 330 PRO   ( 340-)  A   -63.0 half-chair C-beta/C-alpha (-54 degrees)
 334 PRO   ( 344-)  A  -139.1 envelop C-delta (-144 degrees)
 348 PRO   ( 358-)  A   100.6 envelop C-beta (108 degrees)
 372 PRO   ( 382-)  A   102.2 envelop C-beta (108 degrees)
 438 PRO   ( 448-)  A   -62.5 half-chair C-beta/C-alpha (-54 degrees)
 505 PRO   ( 515-)  A    23.5 half-chair N/C-delta (18 degrees)
 596 PRO   (  46-)  B   114.3 envelop C-beta (108 degrees)
 648 PRO   (  98-)  B   -58.3 half-chair C-beta/C-alpha (-54 degrees)
 660 PRO   ( 110-)  B   -54.0 half-chair C-beta/C-alpha (-54 degrees)
 722 PRO   (   5-)  C    25.9 half-chair N/C-delta (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.

 755 CU1   ( 803-)  A     CU   <->  758 CMO   ( 563-)  A      C      1.24    1.96  INTRA BL
 223 HIS   ( 233-)  A      NE2 <->  227 TYR   ( 237-)  A      CE2    1.22    1.88  INTRA BL
 223 HIS   ( 233-)  A      CD2 <->  227 TYR   ( 237-)  A      CE2    0.62    2.58  INTRA BL
 223 HIS   ( 233-)  A      NE2 <->  227 TYR   ( 237-)  A      CZ     0.55    2.55  INTRA BL
 691 ARG   ( 141-)  B      O   <->  695 TYR   ( 145-)  B      OH     0.36    2.04  INTRA BF
 439 ARG   ( 449-)  A      NH2 <->  756 HAS   ( 801-)  A      CGA    0.36    2.74  INTRA BL
 449 ALA   ( 459-)  A      O   <->  696 ARG   ( 146-)  B      NH2    0.32    2.38  INTRA BF
 636 PHE   (  86-)  B      O   <->  638 PHE   (  88-)  B      N      0.32    2.38  INTRA BL
  62 HIS   (  72-)  A      NE2 <->  759 HEM   ( 800-)  A      NB     0.32    2.68  INTRA BL
 223 HIS   ( 233-)  A      ND1 <->  758 CMO   ( 563-)  A      C      0.31    2.79  INTRA BL
 743 VAL   (  26-)  C      O   <->  747 PHE   (  30-)  C      N      0.29    2.41  INTRA BL
 272 HIS   ( 282-)  A      CD2 <->  273 HIS   ( 283-)  A      CD2    0.28    2.92  INTRA BL
 267 THR   ( 277-)  A      N   <->  268 PRO   ( 278-)  A      CD     0.26    2.74  INTRA BL
 664 HIS   ( 114-)  B      ND1 <->  710 MET   ( 160-)  B      SD     0.25    3.05  INTRA BL
 252 ASP   ( 262-)  A      OD1 <->  256 ARG   ( 266-)  A      NE     0.24    2.46  INTRA BL
 272 HIS   ( 282-)  A      NE2 <->  273 HIS   ( 283-)  A      NE2    0.24    2.76  INTRA BL
 395 LEU   ( 405-)  A      N   <->  396 PRO   ( 406-)  A      CD     0.23    2.77  INTRA BF
 277 ASP   ( 287-)  A      O   <->  285 LYS   ( 295-)  A      NZ     0.23    2.47  INTRA BL
 231 LEU   ( 241-)  A      O   <->  235 ALA   ( 245-)  A      N      0.22    2.48  INTRA BL
 314 GLY   ( 324-)  A      CA  <->  329 LEU   ( 339-)  A      CD1    0.22    2.98  INTRA BF
  35 ASN   (  45-)  A      ND2 <->   55 TYR   (  65-)  A      CZ     0.22    2.88  INTRA BL
 426 ALA   ( 436-)  A      O   <->  430 HIS   ( 440-)  A      ND1    0.21    2.49  INTRA BL
 515 ASP   ( 525-)  A      O   <->  517 ILE   ( 527-)  A      N      0.21    2.49  INTRA BL
 311 GLU   ( 321-)  A      O   <->  315 ARG   ( 325-)  A      CG     0.21    2.59  INTRA BF
 440 ARG   ( 450-)  A      NE  <->  759 HEM   ( 800-)  A      O2D    0.21    2.49  INTRA BL
And so on for a total of 160 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 320 ARG   ( 330-)  A      -8.04
 691 ARG   ( 141-)  B      -6.96
 487 ARG   ( 497-)  A      -6.74
 690 LYS   ( 140-)  B      -6.08
 317 ARG   ( 327-)  A      -6.05
 720 GLU   (   3-)  C      -5.92
 439 ARG   ( 449-)  A      -5.85
 322 LEU   ( 332-)  A      -5.82
 205 LEU   ( 215-)  A      -5.69
  53 GLN   (  63-)  A      -5.60
 207 GLU   ( 217-)  A      -5.58
 445 GLN   ( 455-)  A      -5.53
 602 ARG   (  52-)  B      -5.42
 244 GLN   ( 254-)  A      -5.32
 609 ARG   (  59-)  B      -5.27

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.

 609 ARG   (  59-)  B       611 - GLU     61- ( B)         -4.59

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

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.

 449 ALA   ( 459-)  A   -2.95
 546 VAL   ( 556-)  A   -2.53
 620 ALA   (  70-)  B   -2.52

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.

 362 ASP   ( 372-)  A     -  365 VAL   ( 375-)  A        -1.84

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 288 HIS   ( 298-)  A
 667 HIS   ( 117-)  B
 672 ASN   ( 122-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   1 VAL   (  11-)  A      N
   2 TYR   (  12-)  A      N
   3 GLU   (  13-)  A      N
  31 PHE   (  41-)  A      N
  32 GLN   (  42-)  A      NE2
  38 ASN   (  48-)  A      ND2
  51 PHE   (  61-)  A      N
  55 TYR   (  65-)  A      OH
  57 GLN   (  67-)  A      NE2
  66 ASN   (  76-)  A      ND2
  92 ASN   ( 102-)  A      N
 100 TRP   ( 110-)  A      NE1
 119 ALA   ( 129-)  A      N
 120 THR   ( 130-)  A      N
 123 TYR   ( 133-)  A      N
 136 TYR   ( 146-)  A      OH
 158 ARG   ( 168-)  A      NH1
 201 TRP   ( 211-)  A      NE1
 215 ARG   ( 225-)  A      NE
 215 ARG   ( 225-)  A      NH1
 227 TYR   ( 237-)  A      OH
 234 TYR   ( 244-)  A      OH
 248 LYS   ( 258-)  A      N
 251 SER   ( 261-)  A      N
 269 VAL   ( 279-)  A      N
And so on for a total of 71 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.

   3 GLU   (  13-)  A      OE1
  32 GLN   (  42-)  A      OE1
 193 GLU   ( 203-)  A      OE1
 274 GLN   ( 284-)  A      OE1
 277 ASP   ( 287-)  A      OD1
 362 ASP   ( 372-)  A      OD1
 366 HIS   ( 376-)  A      ND1
 378 GLN   ( 388-)  A      OE1
 430 HIS   ( 440-)  A      NE2
 460 ASN   ( 470-)  A      OD1
 619 GLN   (  69-)  B      OE1
 649 GLN   (  99-)  B      OE1
 667 HIS   ( 117-)  B      NE2
 672 ASN   ( 122-)  B      OD1
 676 GLU   ( 126-)  B      OE1

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.

 332 ASP   ( 342-)  A   H-bonding suggests Asn
 507 ASP   ( 517-)  A   H-bonding suggests Asn
 661 ASP   ( 111-)  B   H-bonding suggests Asn
 681 GLU   ( 131-)  B   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 :  -0.865
  2nd generation packing quality :  -0.977
  Ramachandran plot appearance   :  -4.029 (bad)
  chi-1/chi-2 rotamer normality  :  -3.847 (poor)
  Backbone conformation          :   0.253

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.646 (tight)
  Bond angles                    :   0.775
  Omega angle restraints         :   1.250
  Side chain planarity           :   0.621 (tight)
  Improper dihedral distribution :   0.899
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.155

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.646 (tight)
  Bond angles                    :   0.775
  Omega angle restraints         :   1.250
  Side chain planarity           :   0.621 (tight)
  Improper dihedral distribution :   0.899
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.155
==============

WHAT IF
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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.