WHAT IF Check report

This file was created 2011-12-13 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 pdb1cvu.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 181.036  B   = 133.960  C    = 124.834
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 128.747  B   = 124.834  C    = 128.747
    Alpha=  61.000  Beta=  62.698  Gamma=  61.000

Dimensions of the conventional cell

    A    = 124.834  B   = 133.960  C    = 181.036
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.557
CA-only RMS fit for the two chains : 0.376

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

1127 MAN   ( 673-)  A  -
1128 MAN   ( 674-)  A  -
1129 BOG   ( 702-)  A  -
1130 BOG   ( 703-)  B  -
1131 BOG   ( 704-)  A  -
1132 ACD   ( 701-)  A  -
1133 MAN   (2673-)  B  -
1134 BOG   (2702-)  B  -
1135 ACD   (2701-)  B  -
1136 BOG   (2704-)  B  -
1137 MAN   (2674-)  B  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1114 NAG   ( 661-)  A  -   O4  bound to 1115 NAG   ( 662-)  A  -   C1
1116 NAG   ( 671-)  A  -   O4  bound to 1117 NAG   ( 672-)  A  -   C1
1117 NAG   ( 672-)  A  -   O4  bound to 1127 MAN   ( 673-)  A  -   C1
1119 NAG   (2661-)  B  -   O4  bound to 1120 NAG   (2662-)  B  -   C1
1121 NAG   (2671-)  B  -   O4  bound to 1122 NAG   (2672-)  B  -   C1
1122 NAG   (2672-)  B  -   O4  bound to 1133 MAN   (2673-)  B  -   C1

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: F

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) :130.000

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: F

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

  59 TYR   (  91-)  A
  91 TYR   ( 122-)  A
  99 TYR   ( 130-)  A
 116 TYR   ( 147-)  A
 223 TYR   ( 254-)  A
 231 TYR   ( 262-)  A
 244 TYR   ( 275-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 378 TYR   ( 409-)  A
 444 TYR   ( 475-)  A
 464 TYR   ( 495-)  A
 513 TYR   ( 544-)  A
 611 TYR   (2091-)  B
 643 TYR   (2122-)  B
 651 TYR   (2130-)  B
 668 TYR   (2147-)  B
 775 TYR   (2254-)  B
 783 TYR   (2262-)  B
 894 TYR   (2373-)  B
 906 TYR   (2385-)  B
 923 TYR   (2402-)  B
 930 TYR   (2409-)  B
 996 TYR   (2475-)  B
1016 TYR   (2495-)  B
1065 TYR   (2544-)  B

Warning: Phenylalanine convention problem

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

  20 PHE   (  52-)  A
  64 PHE   (  96-)  A
 156 PHE   ( 187-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 178 PHE   ( 209-)  A
 216 PHE   ( 247-)  A
 254 PHE   ( 285-)  A
 336 PHE   ( 367-)  A
 364 PHE   ( 395-)  A
 439 PHE   ( 470-)  A
 447 PHE   ( 478-)  A
 498 PHE   ( 529-)  A
 519 PHE   ( 550-)  A
 546 PHE   ( 577-)  A
 549 PHE   ( 580-)  A
 572 PHE   (2052-)  B
 616 PHE   (2096-)  B
 708 PHE   (2187-)  B
 719 PHE   (2198-)  B
 722 PHE   (2201-)  B
 730 PHE   (2209-)  B
 768 PHE   (2247-)  B
 806 PHE   (2285-)  B
 888 PHE   (2367-)  B
 991 PHE   (2470-)  B
 999 PHE   (2478-)  B
1050 PHE   (2529-)  B
1071 PHE   (2550-)  B
1101 PHE   (2580-)  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.

 127 ASP   ( 158-)  A
 142 ASP   ( 173-)  A
 218 ASP   ( 249-)  A
 362 ASP   ( 393-)  A
 466 ASP   ( 497-)  A
 679 ASP   (2158-)  B
 694 ASP   (2173-)  B
 770 ASP   (2249-)  B
 914 ASP   (2393-)  B
1018 ASP   (2497-)  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.

 109 GLU   ( 140-)  A
 241 GLU   ( 272-)  A
 277 GLU   ( 308-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 370 GLU   ( 401-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 455 GLU   ( 486-)  A
 489 GLU   ( 520-)  A
 661 GLU   (2140-)  B
 781 GLU   (2260-)  B
 829 GLU   (2308-)  B
 847 GLU   (2326-)  B
 860 GLU   (2339-)  B
 885 GLU   (2364-)  B
1001 GLU   (2480-)  B
1005 GLU   (2484-)  B
1007 GLU   (2486-)  B
1011 GLU   (2490-)  B
1041 GLU   (2520-)  B

Error: Decreasing residue numbers

At least one residue in each of the chains mentioned below has a residue number that is lower than the previous residue in that chain ('-' represents a chain without chain identifier).

Chain identifier(s): 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.

 172 GLN   ( 203-)  A      CD   OE1   1.36    6.6
1113 SER   (2603-)  F      C    O     1.41    9.0

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.

 117 TYR   ( 148-)  A      N    CA   C    97.01   -5.1
 172 GLN   ( 203-)  A      CA   CB   CG  105.93   -4.1
 172 GLN   ( 203-)  A      CG   CD   NE2 109.62   -4.5
 173 HIS   ( 204-)  A      CG   ND1  CE1 109.66    4.1
 615 HIS   (2095-)  B      CG   ND1  CE1 109.61    4.0
 654 HIS   (2133-)  B      CG   ND1  CE1 109.61    4.0
 669 TYR   (2148-)  B      N    CA   C    97.60   -4.9
 761 ARG   (2240-)  B      CB   CG   CD  105.73   -4.2
 763 HIS   (2242-)  B      CG   ND1  CE1 109.70    4.1
 794 MET   (2273-)  B      N    CA   C    97.91   -4.7
 907 HIS   (2386-)  B      CG   ND1  CE1 109.85    4.2
1113 SER   (2603-)  F      N    CA   C   129.66    6.6
1113 SER   (2603-)  F      CA   C    O   144.95   14.2

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.

 109 GLU   ( 140-)  A
 127 ASP   ( 158-)  A
 142 ASP   ( 173-)  A
 218 ASP   ( 249-)  A
 241 GLU   ( 272-)  A
 277 GLU   ( 308-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 370 GLU   ( 401-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 455 GLU   ( 486-)  A
 466 ASP   ( 497-)  A
 489 GLU   ( 520-)  A
 661 GLU   (2140-)  B
 679 ASP   (2158-)  B
 694 ASP   (2173-)  B
 770 ASP   (2249-)  B
 781 GLU   (2260-)  B
 829 GLU   (2308-)  B
 847 GLU   (2326-)  B
 860 GLU   (2339-)  B
 885 GLU   (2364-)  B
 914 ASP   (2393-)  B
1001 GLU   (2480-)  B
1005 GLU   (2484-)  B
1007 GLU   (2486-)  B
1011 GLU   (2490-)  B
1018 ASP   (2497-)  B
1041 GLU   (2520-)  B

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.

1113 SER   (2603-)  F    6.88
 117 TYR   ( 148-)  A    5.41
 642 SER   (2121-)  B    5.31
 669 TYR   (2148-)  B    5.19
 702 VAL   (2181-)  B    5.15
  90 SER   ( 121-)  A    5.01
 150 VAL   ( 181-)  A    4.93
 797 PRO   (2276-)  B    4.26
 664 SER   (2143-)  B    4.24
 718 MET   (2197-)  B    4.12
 794 MET   (2273-)  B    4.04

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 : 1.502

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.

 930 TYR   (2409-)  B    -3.6
 627 PRO   (2106-)  B    -2.8
  75 PRO   ( 106-)  A    -2.7
 919 GLU   (2398-)  B    -2.6
1035 PRO   (2514-)  B    -2.6
 581 ARG   (2061-)  B    -2.6
  29 ARG   (  61-)  A    -2.6
 483 PRO   ( 514-)  A    -2.5
 428 LYS   ( 459-)  A    -2.5
 699 LEU   (2178-)  B    -2.5
 147 LEU   ( 178-)  A    -2.5
1005 GLU   (2484-)  B    -2.4
 453 GLU   ( 484-)  A    -2.4
 547 THR   ( 578-)  A    -2.4
1099 THR   (2578-)  B    -2.4
 980 LYS   (2459-)  B    -2.4
  64 PHE   (  96-)  A    -2.4
 616 PHE   (2096-)  B    -2.4
 399 ILE   ( 430-)  A    -2.3
 951 ILE   (2430-)  B    -2.3
 411 ILE   ( 442-)  A    -2.3
 594 PHE   (2074-)  B    -2.3
 963 ILE   (2442-)  B    -2.3
 548 SER   ( 579-)  A    -2.2
 378 TYR   ( 409-)  A    -2.2
 503 LEU   ( 534-)  A    -2.2
1055 LEU   (2534-)  B    -2.2
 685 GLY   (2164-)  B    -2.2
 133 GLY   ( 164-)  A    -2.2
1100 SER   (2579-)  B    -2.1
 516 PRO   ( 547-)  A    -2.1
 140 LEU   ( 171-)  A    -2.1
 576 LYS   (2056-)  B    -2.1
  24 LYS   (  56-)  A    -2.1
 692 LEU   (2171-)  B    -2.1
 564 ARG   (2044-)  B    -2.1
 927 GLN   (2406-)  B    -2.1
 585 TYR   (2065-)  B    -2.1
 812 VAL   (2291-)  B    -2.1
  12 ARG   (  44-)  A    -2.1
1068 PRO   (2547-)  B    -2.0
 574 GLN   (2054-)  B    -2.0
  22 GLN   (  54-)  A    -2.0
 260 VAL   ( 291-)  A    -2.0
 773 LEU   (2252-)  B    -2.0
 221 LEU   ( 252-)  A    -2.0
 589 CYS   (2069-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  12 ARG   (  44-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  90 SER   ( 121-)  A  Poor phi/psi
  91 TYR   ( 122-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 239 GLN   ( 270-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
 378 TYR   ( 409-)  A  Poor phi/psi
 440 SER   ( 471-)  A  Poor phi/psi
 465 SER   ( 496-)  A  Poor phi/psi
 484 ASP   ( 515-)  A  Poor phi/psi
 514 TRP   ( 545-)  A  Poor phi/psi
 564 ARG   (2044-)  B  Poor phi/psi
 581 ARG   (2061-)  B  Poor phi/psi
 642 SER   (2121-)  B  Poor phi/psi
 643 TYR   (2122-)  B  Poor phi/psi
 647 SER   (2126-)  B  PRO omega poor
 650 THR   (2129-)  B  Poor phi/psi
 751 LEU   (2230-)  B  Poor phi/psi
 768 PHE   (2247-)  B  Poor phi/psi
 770 ASP   (2249-)  B  Poor phi/psi
 791 GLN   (2270-)  B  Poor phi/psi
 794 MET   (2273-)  B  Poor phi/psi
 919 GLU   (2398-)  B  Poor phi/psi
 930 TYR   (2409-)  B  Poor phi/psi
 992 SER   (2471-)  B  Poor phi/psi
1017 SER   (2496-)  B  Poor phi/psi
1036 ASP   (2515-)  B  Poor phi/psi
1066 TRP   (2545-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.694

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 : -3.694

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.

 420 SER   ( 451-)  A    0.38
 972 SER   (2451-)  B    0.38
 499 SER   ( 530-)  A    0.40
1051 SER   (2530-)  B    0.40

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!

   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  12 ARG   (  44-)  A      0
  21 ASP   (  53-)  A      0
  22 GLN   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 PHE   (  64-)  A      0
  33 TYR   (  65-)  A      0
  35 GLU   (  67-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  92 LEU   ( 123-)  A      0
  94 ASP   ( 125-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
  98 THR   ( 129-)  A      0
  99 TYR   ( 130-)  A      0
And so on for a total of 421 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 : 1.310

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!

 131 PRO   ( 162-)  A   1.70   13
 683 PRO   (2162-)  B   1.69   13

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]

 443 PRO   ( 474-)  A    0.17 LOW
 545 PRO   ( 576-)  A    0.12 LOW
 801 PRO   (2280-)  B    0.13 LOW
 995 PRO   (2474-)  B    0.18 LOW
1097 PRO   (2576-)  B    0.11 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].

  75 PRO   ( 106-)  A   118.7 half-chair C-beta/C-alpha (126 degrees)
 245 PRO   ( 276-)  A  -117.3 half-chair C-delta/C-gamma (-126 degrees)
 507 PRO   ( 538-)  A  -119.6 half-chair C-delta/C-gamma (-126 degrees)
 627 PRO   (2106-)  B   120.5 half-chair C-beta/C-alpha (126 degrees)
 798 PRO   (2277-)  B  -112.3 envelop C-gamma (-108 degrees)
1059 PRO   (2538-)  B  -117.9 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.

1133 MAN   (2673-)  B      O6  <-> 1137 MAN   (2674-)  B      C1     0.91    1.49  INTRA BF
1133 MAN   (2673-)  B      C6  <-> 1137 MAN   (2674-)  B      C1     0.85    2.35  INTRA BF
 737 ARG   (2216-)  B      NH1 <-> 1122 NAG   (2672-)  B      C7     0.63    2.47  INTRA BF
1107 THR   (2597-)  F      CG2 <-> 1111 ASN   (2601-)  F      ND2    0.59    2.51  INTRA BF
 732 LYS   (2211-)  B      NZ  <->  757 GLU   (2236-)  B      CG     0.41    2.69  INTRA BL
 814 GLY   (2293-)  B      O   <->  932 ASN   (2411-)  B      ND2    0.40    2.30  INTRA BF
 180 LYS   ( 211-)  A      NZ  <->  205 GLU   ( 236-)  A      CG     0.40    2.70  INTRA BL
1113 SER   (2603-)  F      CA  <-> 1126 SER   (2603-)  F      O''    0.37    1.53  INTRA BF
 761 ARG   (2240-)  B      NH2 <->  794 MET   (2273-)  B      CE     0.36    2.74  INTRA BF
 230 VAL   ( 261-)  A      O   <->  276 ARG   ( 307-)  A      NH1    0.26    2.44  INTRA BL
 829 GLU   (2308-)  B      CD  <->  832 ARG   (2311-)  B      NH1    0.25    2.85  INTRA BL
1122 NAG   (2672-)  B      C6  <-> 1133 MAN   (2673-)  B      C1     0.25    2.95  INTRA BF
 559 ASN   (2039-)  B      N   <->  560 PRO   (2040-)  B      CD     0.25    2.75  INTRA
1117 NAG   ( 672-)  A      C6  <-> 1127 MAN   ( 673-)  A      C1     0.24    2.96  INTRA BF
 277 GLU   ( 308-)  A      CD  <->  280 ARG   ( 311-)  A      NH1    0.24    2.86  INTRA BL
  90 SER   ( 121-)  A      O   <->   92 LEU   ( 123-)  A      N      0.24    2.46  INTRA BF
 642 SER   (2121-)  B      O   <->  644 LEU   (2123-)  B      N      0.24    2.46  INTRA BF
 622 ILE   (2102-)  B      CG1 <->  623 VAL   (2103-)  B      N      0.23    2.77  INTRA BF
   7 ASN   (  39-)  A      N   <->    8 PRO   (  40-)  A      CD     0.23    2.77  INTRA BL
  70 ILE   ( 102-)  A      CG1 <->   71 VAL   ( 103-)  A      N      0.22    2.78  INTRA BF
 277 GLU   ( 308-)  A      OE2 <->  280 ARG   ( 311-)  A      NH1    0.22    2.48  INTRA BL
 909 HIS   (2388-)  B      N   <->  910 PRO   (2389-)  B      CD     0.21    2.79  INTRA BL
 357 HIS   ( 388-)  A      N   <->  358 PRO   ( 389-)  A      CD     0.21    2.79  INTRA BL
  29 ARG   (  61-)  A      NH2 <-> 1138 HOH   (3003 )  A      O      0.21    2.49  INTRA
 221 LEU   ( 252-)  A      O   <->  279 GLN   ( 310-)  A      NE2    0.21    2.49  INTRA BL
And so on for a total of 222 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.

 546 PHE   ( 577-)  A      -6.58
 799 HIS   (2278-)  B      -6.58
 247 HIS   ( 278-)  A      -6.56
  29 ARG   (  61-)  A      -6.43
 581 ARG   (2061-)  B      -6.43
1098 PHE   (2577-)  B      -5.90
 795 ILE   (2274-)  B      -5.90
 138 LYS   ( 169-)  A      -5.63
 690 LYS   (2169-)  B      -5.62
  20 PHE   (  52-)  A      -5.61
 386 HIS   ( 417-)  A      -5.56
 572 PHE   (2052-)  B      -5.56
 796 TYR   (2275-)  B      -5.56
 938 HIS   (2417-)  B      -5.52
 185 ARG   ( 216-)  A      -5.49
 737 ARG   (2216-)  B      -5.42
 105 TYR   ( 136-)  A      -5.32
 793 GLU   (2272-)  B      -5.31
 397 ARG   ( 428-)  A      -5.28
 949 ARG   (2428-)  B      -5.28
 184 LYS   ( 215-)  A      -5.25
 768 PHE   (2247-)  B      -5.24
 657 TYR   (2136-)  B      -5.23
 736 LYS   (2215-)  B      -5.22
 891 GLN   (2370-)  B      -5.17
 216 PHE   ( 247-)  A      -5.13
 339 GLN   ( 370-)  A      -5.11
 708 PHE   (2187-)  B      -5.09
 156 PHE   ( 187-)  A      -5.09
 201 HIS   ( 232-)  A      -5.05
 154 ARG   ( 185-)  A      -5.04
 753 HIS   (2232-)  B      -5.02

Warning: Abnormal packing environment for sequential residues

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

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

 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -4.88
 690 LYS   (2169-)  B       692 - LEU   2171- ( B)         -4.87

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

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.

 746 GLY   (2225-)  B   -3.13
 194 GLY   ( 225-)  A   -3.13
 154 ARG   ( 185-)  A   -2.77
 252 LEU   ( 283-)  A   -2.75
 886 LEU   (2365-)  B   -2.68
 334 LEU   ( 365-)  A   -2.68
 706 ARG   (2185-)  B   -2.66
 657 TYR   (2136-)  B   -2.66
 105 TYR   ( 136-)  A   -2.62
 644 LEU   (2123-)  B   -2.60
  92 LEU   ( 123-)  A   -2.58
 812 VAL   (2291-)  B   -2.57

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.

 152 LEU   ( 183-)  A     -  155 GLU   ( 186-)  A        -2.06
 175 THR   ( 206-)  A     -  178 PHE   ( 209-)  A        -1.72
 704 LEU   (2183-)  B     -  707 GLU   (2186-)  B        -2.13
 727 THR   (2206-)  B     -  730 PHE   (2209-)  B        -1.72

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

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.

1138 HOH   (3047 )  A      O     75.55   -2.56    9.19
1138 HOH   (3050 )  A      O     75.60    0.64   15.59
1138 HOH   (3118 )  A      O     73.23   -1.28   22.84
1138 HOH   (3556 )  A      O     94.72   25.59   27.31
1138 HOH   (3577 )  A      O     90.55   41.91   30.67
1138 HOH   (3640 )  A      O     62.02    0.48   17.29
1138 HOH   (3674 )  A      O     54.73    0.34   21.41
1138 HOH   (3708 )  A      O     68.68   29.51   -1.52
1138 HOH   (3743 )  A      O     63.90   31.65   -1.45
1139 HOH   (3630 )  B      O     44.56   46.92   65.32
1139 HOH   (3757 )  B      O      6.21   49.17   33.10

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.

1138 HOH   (3004 )  A      O
1138 HOH   (3090 )  A      O
1138 HOH   (3205 )  A      O
1138 HOH   (3210 )  A      O
1138 HOH   (3678 )  A      O
1139 HOH   (3227 )  B      O
1139 HOH   (3255 )  B      O
1139 HOH   (3299 )  B      O
1139 HOH   (3322 )  B      O
1139 HOH   (3324 )  B      O
1139 HOH   (3363 )  B      O
1139 HOH   (3750 )  B      O
Bound group on Asn; dont flip   36 ASN  (  68-) A
Bound to: 1114 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 1116 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 1118 NAG  ( 681-) A
Bound group on Asn; dont flip  588 ASN  (2068-) B
Bound to: 1119 NAG  (2661-) B
Bound group on Asn; dont flip  665 ASN  (2144-) B
Bound to: 1121 NAG  (2671-) B
Bound group on Asn; dont flip  931 ASN  (2410-) B
Bound to: 1123 NAG  (2681-) B

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.

   2 ASN   (  34-)  A
 100 ASN   ( 131-)  A
 172 GLN   ( 203-)  A
 287 GLN   ( 318-)  A
 338 GLN   ( 369-)  A
 386 HIS   ( 417-)  A
 398 GLN   ( 429-)  A
 433 ASN   ( 464-)  A
 554 ASN   (2034-)  B
 621 ASN   (2101-)  B
 652 ASN   (2131-)  B
 803 ASN   (2282-)  B
 890 GLN   (2369-)  B
 938 HIS   (2417-)  B
 950 GLN   (2429-)  B
 985 ASN   (2464-)  B
1102 ASN   (2581-)  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.

  36 ASN   (  68-)  A      N
 100 ASN   ( 131-)  A      ND2
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 135 LYS   ( 166-)  A      N
 145 GLU   ( 176-)  A      N
 177 GLN   ( 208-)  A      NE2
 181 THR   ( 212-)  A      OG1
 184 LYS   ( 215-)  A      N
 191 ARG   ( 222-)  A      NE
 206 THR   ( 237-)  A      N
 217 LYS   ( 248-)  A      N
 266 GLY   ( 297-)  A      N
 276 ARG   ( 307-)  A      NH1
 279 GLN   ( 310-)  A      NE2
 291 GLU   ( 322-)  A      N
 317 TYR   ( 348-)  A      OH
 326 PHE   ( 357-)  A      N
 357 HIS   ( 388-)  A      N
 383 LEU   ( 414-)  A      N
 403 VAL   ( 434-)  A      N
 446 SER   ( 477-)  A      N
 499 SER   ( 530-)  A      OG
 652 ASN   (2131-)  B      ND2
 657 TYR   (2136-)  B      N
And so on for a total of 58 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 211 HIS   ( 242-)  A      ND1
 308 GLU   ( 339-)  A      OE2
 351 ASN   ( 382-)  A      OD1
 522 GLU   ( 553-)  A      OE1
 661 GLU   (2140-)  B      OE2
 763 HIS   (2242-)  B      ND1
 860 GLU   (2339-)  B      OE2
 903 ASN   (2382-)  B      OD1
1074 GLU   (2553-)  B      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1138 HOH   (3117 )  A      O  0.87  K  5
1138 HOH   (3122 )  A      O  0.93  K  5
1139 HOH   (3420 )  B      O  1.04  K  4
1139 HOH   (3461 )  B      O  0.90  K  4

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  21 ASP   (  53-)  A   H-bonding suggests Asn; but Alt-Rotamer
  41 GLU   (  73-)  A   H-bonding suggests Gln
 368 ASP   ( 399-)  A   H-bonding suggests Asn; but Alt-Rotamer
 661 GLU   (2140-)  B   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.214
  2nd generation packing quality :  -1.615
  Ramachandran plot appearance   :  -1.993
  chi-1/chi-2 rotamer normality  :  -3.694 (poor)
  Backbone conformation          :  -1.099

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.659 (tight)
  Omega angle restraints         :   0.238 (tight)
  Side chain planarity           :   0.272 (tight)
  Improper dihedral distribution :   0.653
  B-factor distribution          :   0.450
  Inside/Outside distribution    :   1.100

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.659 (tight)
  Omega angle restraints         :   0.238 (tight)
  Side chain planarity           :   0.272 (tight)
  Improper dihedral distribution :   0.653
  B-factor distribution          :   0.450
  Inside/Outside distribution    :   1.100
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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      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,
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      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.