WHAT IF Check report

This file was created 2013-05-09 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 pdb1j37.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  94.912  B   = 121.223  C    =  94.740
    Alpha=  90.000  Beta=  99.390  Gamma=  90.000

Dimensions of a reduced cell

    A    =  94.740  B   =  94.912  C    = 121.223
    Alpha=  90.000  Beta=  90.000  Gamma=  99.390

Dimensions of the conventional cell

    A    = 122.678  B   = 144.631  C    = 121.223
    Alpha=  90.000  Beta=  90.000  Gamma=  89.895

Transformation to conventional cell

 | -1.000000  0.000000 -1.000000|
 | -1.000000  0.000000  1.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Warning: New symmetry found

In the conventional cell, independent molecules in the asymmetric unit seemingly become symmetry relatives. This fact needs manual checking.

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.

1201 X8Z   ( 802-)  B  -
1202 X8Z   ( 801-)  A  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

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

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

 206 TYR   ( 228-)  A  -   CB
 207 GLN   ( 229-)  A  -   CB
 208 GLN   ( 230-)  A  -   CB
 210 HIS   ( 232-)  A  -   CB
 212 TYR   ( 234-)  A  -   CB
 213 VAL   ( 235-)  A  -   CB
 214 ARG   ( 236-)  A  -   CB
 215 PHE   ( 237-)  A  -   CB
 216 ARG   ( 238-)  A  -   CB
 405 ARG   ( 427-)  A  -   CB
 406 ILE   ( 428-)  A  -   CB
 407 ASN   ( 429-)  A  -   CB
 408 GLN   ( 430-)  A  -   CB
 409 LEU   ( 431-)  A  -   CB
 410 PHE   ( 432-)  A  -   CB
 411 LEU   ( 433-)  A  -   CB
 412 THR   ( 434-)  A  -   CB
 413 ALA   ( 435-)  A  -   CB
 414 LEU   ( 436-)  A  -   CB
 415 ASP   ( 437-)  A  -   CB
 558 LYS   ( 580-)  A  -   CB
 559 ALA   ( 581-)  A  -   CB
 560 ILE   ( 582-)  A  -   CB
 562 GLU   ( 584-)  A  -   CB
 563 TYR   ( 585-)  A  -   CB
And so on for a total of 52 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

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

 206 TYR   ( 228-)  A  -   N
 206 TYR   ( 228-)  A  -   CA
 206 TYR   ( 228-)  A  -   C
 206 TYR   ( 228-)  A  -   O
 207 GLN   ( 229-)  A  -   N
 207 GLN   ( 229-)  A  -   CA
 207 GLN   ( 229-)  A  -   C
 207 GLN   ( 229-)  A  -   O
 208 GLN   ( 230-)  A  -   N
 208 GLN   ( 230-)  A  -   CA
 208 GLN   ( 230-)  A  -   C
 208 GLN   ( 230-)  A  -   O
 209 ILE   ( 231-)  A  -   N
 209 ILE   ( 231-)  A  -   CA
 209 ILE   ( 231-)  A  -   C
 209 ILE   ( 231-)  A  -   O
 210 HIS   ( 232-)  A  -   N
 210 HIS   ( 232-)  A  -   CA
 210 HIS   ( 232-)  A  -   C
 210 HIS   ( 232-)  A  -   O
 211 GLY   ( 233-)  A  -   N
 211 GLY   ( 233-)  A  -   CA
 211 GLY   ( 233-)  A  -   C
 211 GLY   ( 233-)  A  -   O
 212 TYR   ( 234-)  A  -   N
And so on for a total of 256 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: What type of B-factor?

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

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

Crystal temperature (K) :123.000

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

 212 TYR   ( 234-)  A
 272 TYR   ( 294-)  A
 322 TYR   ( 344-)  A
 352 TYR   ( 374-)  A
 454 TYR   ( 476-)  A
 810 TYR   ( 234-)  B
 870 TYR   ( 294-)  B
 920 TYR   ( 344-)  B
 950 TYR   ( 374-)  B
1052 TYR   ( 476-)  B

Warning: Phenylalanine convention problem

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

 284 PHE   ( 306-)  A
 371 PHE   ( 393-)  A
 410 PHE   ( 432-)  A
 434 PHE   ( 456-)  A
 489 PHE   ( 511-)  A
 495 PHE   ( 517-)  A
 882 PHE   ( 306-)  B
 969 PHE   ( 393-)  B
1008 PHE   ( 432-)  B
1032 PHE   ( 456-)  B
1087 PHE   ( 511-)  B
1093 PHE   ( 517-)  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.

  57 ASP   (  79-)  A
 112 ASP   ( 134-)  A
 136 ASP   ( 158-)  A
 188 ASP   ( 210-)  A
 296 ASP   ( 318-)  A
 311 ASP   ( 333-)  A
 320 ASP   ( 342-)  A
 325 ASP   ( 347-)  A
 397 ASP   ( 419-)  A
 402 ASP   ( 424-)  A
 427 ASP   ( 449-)  A
 452 ASP   ( 474-)  A
 479 ASP   ( 501-)  A
 519 ASP   ( 541-)  A
 544 ASP   ( 566-)  A
 655 ASP   (  79-)  B
 710 ASP   ( 134-)  B
 734 ASP   ( 158-)  B
 786 ASP   ( 210-)  B
 894 ASP   ( 318-)  B
 909 ASP   ( 333-)  B
 918 ASP   ( 342-)  B
 923 ASP   ( 347-)  B
 995 ASP   ( 419-)  B
1000 ASP   ( 424-)  B
1025 ASP   ( 449-)  B
1050 ASP   ( 474-)  B
1077 ASP   ( 501-)  B
1117 ASP   ( 541-)  B
1142 ASP   ( 566-)  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.

   8 GLU   (  30-)  A
  21 GLU   (  43-)  A
  46 GLU   (  68-)  A
  69 GLU   (  91-)  A
 128 GLU   ( 150-)  A
 138 GLU   ( 160-)  A
 247 GLU   ( 269-)  A
 266 GLU   ( 288-)  A
 403 GLU   ( 425-)  A
 437 GLU   ( 459-)  A
 453 GLU   ( 475-)  A
 552 GLU   ( 574-)  A
 562 GLU   ( 584-)  A
 606 GLU   (  30-)  B
 619 GLU   (  43-)  B
 644 GLU   (  68-)  B
 667 GLU   (  91-)  B
 726 GLU   ( 150-)  B
 736 GLU   ( 160-)  B
 845 GLU   ( 269-)  B
 864 GLU   ( 288-)  B
1001 GLU   ( 425-)  B
1035 GLU   ( 459-)  B
1051 GLU   ( 475-)  B
1150 GLU   ( 574-)  B
1160 GLU   ( 584-)  B

Geometric checks

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

 |  0.999795 -0.000220 -0.000468|
 | -0.000220  0.998012  0.000231|
 | -0.000468  0.000231  0.999727|
Proposed new scale matrix

 |  0.010539  0.000002  0.001747|
 |  0.000002  0.008265 -0.000002|
 |  0.000005 -0.000002  0.010701|
With corresponding cell

    A    =  94.893  B   = 120.986  C    =  94.733
    Alpha=  89.970  Beta=  99.441  Gamma=  90.025

The CRYST1 cell dimensions

    A    =  94.912  B   = 121.223  C    =  94.740
    Alpha=  90.000  Beta=  99.390  Gamma=  90.000

Variance: 40.187
(Under-)estimated Z-score: 4.672

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.

 210 HIS   ( 232-)  A      CG   ND1  CE1 109.61    4.0
 314 CYS   ( 336-)  A      CA   CB   SG  103.33   -4.8
 402 ASP   ( 424-)  A      N    CA   C    99.81   -4.1
 435 ARG   ( 457-)  A      N    CA   C    97.62   -4.9
 912 CYS   ( 336-)  B      CA   CB   SG  105.07   -4.1
1000 ASP   ( 424-)  B      N    CA   C    99.74   -4.1
1033 ARG   ( 457-)  B      N    CA   C    97.56   -4.9

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.

   8 GLU   (  30-)  A
  21 GLU   (  43-)  A
  46 GLU   (  68-)  A
  57 ASP   (  79-)  A
  69 GLU   (  91-)  A
 112 ASP   ( 134-)  A
 128 GLU   ( 150-)  A
 136 ASP   ( 158-)  A
 138 GLU   ( 160-)  A
 188 ASP   ( 210-)  A
 247 GLU   ( 269-)  A
 266 GLU   ( 288-)  A
 296 ASP   ( 318-)  A
 311 ASP   ( 333-)  A
 320 ASP   ( 342-)  A
 325 ASP   ( 347-)  A
 397 ASP   ( 419-)  A
 402 ASP   ( 424-)  A
 403 GLU   ( 425-)  A
 427 ASP   ( 449-)  A
 437 GLU   ( 459-)  A
 452 ASP   ( 474-)  A
 453 GLU   ( 475-)  A
 479 ASP   ( 501-)  A
 519 ASP   ( 541-)  A
And so on for a total of 56 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.

 126 GLU   ( 148-)  A    6.91
 724 GLU   ( 148-)  B    6.82
 404 ALA   ( 426-)  A    5.85
1002 ALA   ( 426-)  B    5.71
 669 LEU   (  93-)  B    5.42
 806 GLN   ( 230-)  B    5.40
 208 GLN   ( 230-)  A    5.36
  71 LEU   (  93-)  A    5.30
1033 ARG   ( 457-)  B    5.15
 435 ARG   ( 457-)  A    5.13
1014 LYS   ( 438-)  B    4.82
1047 LYS   ( 471-)  B    4.66
 416 LYS   ( 438-)  A    4.59
 965 ALA   ( 389-)  B    4.41
 749 ALA   ( 173-)  B    4.41
 151 ALA   ( 173-)  A    4.38
 367 ALA   ( 389-)  A    4.32
 209 ILE   ( 231-)  A    4.32
 807 ILE   ( 231-)  B    4.27
 449 LYS   ( 471-)  A    4.25
1053 SER   ( 477-)  B    4.21
 898 LYS   ( 322-)  B    4.21
 300 LYS   ( 322-)  A    4.13
 752 ALA   ( 176-)  B    4.11
1049 ARG   ( 473-)  B    4.08
 154 ALA   ( 176-)  A    4.08

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 : 1.761

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 : -3.997

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.

 963 THR   ( 387-)  B    -3.2
 365 THR   ( 387-)  A    -3.2
 153 THR   ( 175-)  A    -2.8
 910 LEU   ( 334-)  B    -2.8
 312 LEU   ( 334-)  A    -2.8
 751 THR   ( 175-)  B    -2.7
 593 SER   ( 615-)  A    -2.7
1191 SER   ( 615-)  B    -2.7
 664 TYR   (  88-)  B    -2.6
 594 HIS   ( 616-)  A    -2.6
1192 HIS   ( 616-)  B    -2.5
  66 TYR   (  88-)  A    -2.5
 202 ILE   ( 224-)  A    -2.5
 800 ILE   ( 224-)  B    -2.5
 229 THR   ( 251-)  A    -2.5
 537 GLY   ( 559-)  A    -2.4
1135 GLY   ( 559-)  B    -2.4
 585 ILE   ( 607-)  A    -2.4
1183 ILE   ( 607-)  B    -2.4
 833 HIS   ( 257-)  B    -2.4
 827 THR   ( 251-)  B    -2.3
 931 THR   ( 355-)  B    -2.3
 235 HIS   ( 257-)  A    -2.3
 512 GLU   ( 534-)  A    -2.3
1110 GLU   ( 534-)  B    -2.3
And so on for a total of 58 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.

  67 GLN   (  89-)  A  Poor phi/psi
  69 GLU   (  91-)  A  Poor phi/psi
  70 ASP   (  92-)  A  Poor phi/psi
 116 SER   ( 138-)  A  Poor phi/psi
 119 CYS   ( 141-)  A  Poor phi/psi
 124 ASP   ( 146-)  A  Poor phi/psi
 125 PRO   ( 147-)  A  Poor phi/psi
 174 ASN   ( 196-)  A  Poor phi/psi
 208 GLN   ( 230-)  A  Poor phi/psi
 229 THR   ( 251-)  A  Poor phi/psi
 234 MET   ( 256-)  A  Poor phi/psi
 235 HIS   ( 257-)  A  Poor phi/psi
 242 ALA   ( 264-)  A  Poor phi/psi
 271 ALA   ( 293-)  A  Poor phi/psi
 289 ASN   ( 311-)  A  Poor phi/psi
 323 LEU   ( 345-)  A  Poor phi/psi
 325 ASP   ( 347-)  A  Poor phi/psi
 361 PHE   ( 383-)  A  Poor phi/psi
 368 ASN   ( 390-)  A  Poor phi/psi
 396 LYS   ( 418-)  A  Poor phi/psi
 401 ASP   ( 423-)  A  Poor phi/psi
 402 ASP   ( 424-)  A  Poor phi/psi
 436 GLY   ( 458-)  A  Poor phi/psi
 509 ASP   ( 531-)  A  Poor phi/psi
 511 VAL   ( 533-)  A  Poor phi/psi
And so on for a total of 65 lines.

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 : -3.016

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.

 382 SER   ( 404-)  A    0.35
 157 SER   ( 179-)  A    0.38
 642 SER   (  66-)  B    0.38
  44 SER   (  66-)  A    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 ALA   (  25-)  A      0
  30 SER   (  52-)  A      0
  61 PHE   (  83-)  A      0
  62 GLN   (  84-)  A      0
  63 TRP   (  85-)  A      0
  65 SER   (  87-)  A      0
  67 GLN   (  89-)  A      0
  69 GLU   (  91-)  A      0
  70 ASP   (  92-)  A      0
  83 TYR   ( 105-)  A      0
 114 LYS   ( 136-)  A      0
 116 SER   ( 138-)  A      0
 118 LYS   ( 140-)  A      0
 119 CYS   ( 141-)  A      0
 120 ASP   ( 142-)  A      0
 125 PRO   ( 147-)  A      0
 132 SER   ( 154-)  A      0
 133 LYS   ( 155-)  A      0
 134 SER   ( 156-)  A      0
 135 ARG   ( 157-)  A      0
 137 HIS   ( 159-)  A      0
 153 THR   ( 175-)  A      0
 174 ASN   ( 196-)  A      0
 176 THR   ( 198-)  A      0
 207 GLN   ( 229-)  A      0
And so on for a total of 383 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 : 1.248

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!

1135 GLY   ( 559-)  B   3.28   19
 537 GLY   ( 559-)  A   3.26   19

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...

 593 SER   ( 615-)  A   2.02
1191 SER   ( 615-)  B   1.90

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].

 541 PRO   ( 563-)  A  -129.7 half-chair C-delta/C-gamma (-126 degrees)
1139 PRO   ( 563-)  B  -130.2 half-chair C-delta/C-gamma (-126 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.

 832 MET   ( 256-)  B      O   <->  834 LEU   ( 258-)  B      N      0.62    2.08  INTRA BL
 234 MET   ( 256-)  A      O   <->  236 LEU   ( 258-)  A      N      0.60    2.10  INTRA BL
1117 ASP   ( 541-)  B      O   <-> 1119 TYR   ( 543-)  B      N      0.55    2.15  INTRA
 519 ASP   ( 541-)  A      O   <->  521 TYR   ( 543-)  A      N      0.55    2.15  INTRA
 814 ARG   ( 238-)  B      NH1 <->  849 ILE   ( 273-)  B      O      0.42    2.28  INTRA
1189 VAL   ( 613-)  B      CG2 <-> 1190 SER   ( 614-)  B      N      0.38    2.62  INTRA
 216 ARG   ( 238-)  A      NH1 <->  251 ILE   ( 273-)  A      O      0.36    2.34  INTRA
 591 VAL   ( 613-)  A      CG2 <->  592 SER   ( 614-)  A      N      0.36    2.64  INTRA
 911 VAL   ( 335-)  B      O   <->  928 LYS   ( 352-)  B      NZ     0.34    2.36  INTRA BL
  69 GLU   (  91-)  A      O   <->   71 LEU   (  93-)  A      N      0.34    2.36  INTRA BF
 234 MET   ( 256-)  A      O   <->  235 HIS   ( 257-)  A      ND1    0.34    2.26  INTRA BL
 667 GLU   (  91-)  B      O   <->  669 LEU   (  93-)  B      N      0.33    2.37  INTRA BF
 313 VAL   ( 335-)  A      O   <->  330 LYS   ( 352-)  A      NZ     0.32    2.38  INTRA BL
 368 ASN   ( 390-)  A      OD1 <->  370 GLY   ( 392-)  A      N      0.32    2.38  INTRA BL
 325 ASP   ( 347-)  A      N   <->  357 GLN   ( 379-)  A      NE2    0.31    2.54  INTRA
 923 ASP   ( 347-)  B      N   <->  955 GLN   ( 379-)  B      NE2    0.31    2.54  INTRA
 832 MET   ( 256-)  B      O   <->  833 HIS   ( 257-)  B      ND1    0.31    2.29  INTRA BL
 966 ASN   ( 390-)  B      OD1 <->  968 GLY   ( 392-)  B      N      0.30    2.40  INTRA BL
1117 ASP   ( 541-)  B      C   <-> 1119 TYR   ( 543-)  B      N      0.30    2.60  INTRA
 743 ARG   ( 167-)  B      NH1 <->  744 GLU   ( 168-)  B      OE2    0.30    2.40  INTRA BL
 519 ASP   ( 541-)  A      C   <->  521 TYR   ( 543-)  A      N      0.29    2.61  INTRA
 565 GLU   ( 587-)  A      CD  <->  568 ARG   ( 590-)  A      NH2    0.29    2.81  INTRA
 145 ARG   ( 167-)  A      NH1 <->  146 GLU   ( 168-)  A      OE2    0.29    2.41  INTRA
1163 GLU   ( 587-)  B      CD  <-> 1166 ARG   ( 590-)  B      NH2    0.28    2.82  INTRA
 832 MET   ( 256-)  B      C   <->  834 LEU   ( 258-)  B      N      0.28    2.62  INTRA BL
And so on for a total of 318 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 220 HIS   ( 242-)  A      -5.90
 818 HIS   ( 242-)  B      -5.88
1195 HIS   ( 619-)  B      -5.69
 597 HIS   ( 619-)  A      -5.67
1156 LYS   ( 580-)  B      -5.44
 558 LYS   ( 580-)  A      -5.44
 711 TYR   ( 135-)  B      -5.35
 310 ARG   ( 332-)  A      -5.24
 908 ARG   ( 332-)  B      -5.22
1192 HIS   ( 616-)  B      -5.20
 324 ILE   ( 346-)  A      -5.17
 870 TYR   ( 294-)  B      -5.16
 922 ILE   ( 346-)  B      -5.15
  67 GLN   (  89-)  A      -5.14
 113 TYR   ( 135-)  A      -5.13
 292 LYS   ( 314-)  A      -5.13
 550 ASN   ( 572-)  A      -5.11
 581 HIS   ( 603-)  A      -5.10
1148 ASN   ( 572-)  B      -5.09
   2 GLN   (  24-)  A      -5.08
 272 TYR   ( 294-)  A      -5.07
1179 HIS   ( 603-)  B      -5.05
 305 LYS   ( 327-)  A      -5.05
 890 LYS   ( 314-)  B      -5.04
 665 GLN   (  89-)  B      -5.04
 512 GLU   ( 534-)  A      -5.03
 903 LYS   ( 327-)  B      -5.02
 594 HIS   ( 616-)  A      -5.01
 600 GLN   (  24-)  B      -5.01

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.

 593 SER   ( 615-)  A       597 - HIS    619- ( A)         -4.69
1191 SER   ( 615-)  B      1195 - HIS    619- ( B)         -4.74

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: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: 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.

  11 ASN   (  33-)  A
  74 GLN   (  96-)  A
 104 ASN   ( 126-)  A
 344 HIS   ( 366-)  A
 351 GLN   ( 373-)  A
 355 GLN   ( 377-)  A
 357 GLN   ( 379-)  A
 359 GLN   ( 381-)  A
 388 HIS   ( 410-)  A
 407 ASN   ( 429-)  A
 444 ASN   ( 466-)  A
 492 GLN   ( 514-)  A
 494 GLN   ( 516-)  A
 505 GLN   ( 527-)  A
 517 ASN   ( 539-)  A
 609 ASN   (  33-)  B
 617 ASN   (  41-)  B
 672 GLN   (  96-)  B
 702 ASN   ( 126-)  B
 942 HIS   ( 366-)  B
 949 GLN   ( 373-)  B
 953 GLN   ( 377-)  B
 955 GLN   ( 379-)  B
 957 GLN   ( 381-)  B
 986 HIS   ( 410-)  B
1005 ASN   ( 429-)  B
1042 ASN   ( 466-)  B
1090 GLN   ( 514-)  B
1092 GLN   ( 516-)  B
1103 GLN   ( 527-)  B
1115 ASN   ( 539-)  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.

   3 ALA   (  25-)  A      N
   4 LYS   (  26-)  A      N
   5 GLU   (  27-)  A      N
  29 ARG   (  51-)  A      NE
  61 PHE   (  83-)  A      N
  64 ARG   (  86-)  A      N
  66 TYR   (  88-)  A      N
  67 GLN   (  89-)  A      N
  73 ARG   (  95-)  A      N
  76 LYS   (  98-)  A      N
  90 ASP   ( 112-)  A      N
 111 CYS   ( 133-)  A      N
 112 ASP   ( 134-)  A      N
 119 CYS   ( 141-)  A      N
 126 GLU   ( 148-)  A      N
 137 HIS   ( 159-)  A      N
 138 GLU   ( 160-)  A      N
 144 TRP   ( 166-)  A      NE1
 150 LYS   ( 172-)  A      N
 177 SER   ( 199-)  A      N
 177 SER   ( 199-)  A      OG
 178 GLY   ( 200-)  A      N
 208 GLN   ( 230-)  A      N
 214 ARG   ( 236-)  A      NE
 235 HIS   ( 257-)  A      N
And so on for a total of 129 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.

  19 ASN   (  41-)  A      OD1
 166 ASN   ( 188-)  A      OD1
 210 HIS   ( 232-)  A      ND1
 235 HIS   ( 257-)  A      ND1
 262 ASP   ( 284-)  A      OD1
 331 GLN   ( 353-)  A      OE1
 346 GLU   ( 368-)  A      OE1
 346 GLU   ( 368-)  A      OE2
 519 ASP   ( 541-)  A      OD1
 575 ASN   ( 597-)  A      OD1
 764 ASN   ( 188-)  B      OD1
 808 HIS   ( 232-)  B      ND1
 833 HIS   ( 257-)  B      ND1
 860 ASP   ( 284-)  B      OD1
 929 GLN   ( 353-)  B      OE1
 944 GLU   ( 368-)  B      OE1
 944 GLU   ( 368-)  B      OE2
1117 ASP   ( 541-)  B      OD1
1173 ASN   ( 597-)  B      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.

  57 ASP   (  79-)  A   H-bonding suggests Asn; but Alt-Rotamer
 126 GLU   ( 148-)  A   H-bonding suggests Gln; but Alt-Rotamer
 128 GLU   ( 150-)  A   H-bonding suggests Gln; but Alt-Rotamer
 149 ASP   ( 171-)  A   H-bonding suggests Asn
 283 ASP   ( 305-)  A   H-bonding suggests Asn
 299 ASP   ( 321-)  A   H-bonding suggests Asn
 465 GLU   ( 487-)  A   H-bonding suggests Gln
 467 ASP   ( 489-)  A   H-bonding suggests Asn; but Alt-Rotamer
 572 GLU   ( 594-)  A   H-bonding suggests Gln
 655 ASP   (  79-)  B   H-bonding suggests Asn
 724 GLU   ( 148-)  B   H-bonding suggests Gln
 726 GLU   ( 150-)  B   H-bonding suggests Gln
 747 ASP   ( 171-)  B   H-bonding suggests Asn
 881 ASP   ( 305-)  B   H-bonding suggests Asn
 897 ASP   ( 321-)  B   H-bonding suggests Asn
1063 GLU   ( 487-)  B   H-bonding suggests Gln
1065 ASP   ( 489-)  B   H-bonding suggests Asn; but Alt-Rotamer
1170 GLU   ( 594-)  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 :  -1.166
  2nd generation packing quality :  -1.920
  Ramachandran plot appearance   :  -3.997 (poor)
  chi-1/chi-2 rotamer normality  :  -3.016 (poor)
  Backbone conformation          :  -0.767

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.390 (tight)
  Bond angles                    :   0.697
  Omega angle restraints         :   0.227 (tight)
  Side chain planarity           :   0.287 (tight)
  Improper dihedral distribution :   0.621
  B-factor distribution          :   0.668
  Inside/Outside distribution    :   1.019

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -1.8
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.390 (tight)
  Bond angles                    :   0.697
  Omega angle restraints         :   0.227 (tight)
  Side chain planarity           :   0.287 (tight)
  Improper dihedral distribution :   0.621
  B-factor distribution          :   0.668
  Inside/Outside distribution    :   1.019
==============

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.