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 pdb1ddx.ent

Checks that need to be done early-on in validation

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 : 0.063
CA-only RMS fit for the two chains : 0.042

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

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 D

All-atom RMS fit for the two chains : 0.057
CA-only RMS fit for the two chains : 0.039

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: B and C

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: B and D

All-atom RMS fit for the two chains : 0.057
CA-only RMS fit for the two chains : 0.039

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: B and D

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.

2229 BOG   ( 702-)  A  -         OK
2230 PGX   ( 701-)  A  -
2231 BOG   (1702-)  B  -         OK
2232 PGX   (1701-)  B  -
2233 BOG   (2702-)  C  -         OK
2234 PGX   (3701-)  D  -
2235 BOG   (3702-)  D  -         OK
2236 BOG   (2701-)  C  -         OK

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.

2209 NAG   ( 661-)  A  -   O4  bound to 2210 NAG   ( 662-)  A  -   C1
2213 NAG   (1661-)  B  -   O4  bound to 2214 NAG   (1662-)  B  -   C1
2217 NAG   (2661-)  C  -   O4  bound to 2218 NAG   (2662-)  C  -   C1
2221 NAG   (3661-)  D  -   O4  bound to 2222 NAG   (3662-)  D  -   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: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 3.78

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

Note: B-factor plot

Chain identifier: D

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

  23 TYR   (  55-)  A
  33 TYR   (  65-)  A
  59 TYR   (  91-)  A
  91 TYR   ( 122-)  A
 103 TYR   ( 134-)  A
 231 TYR   ( 262-)  A
 317 TYR   ( 348-)  A
 342 TYR   ( 373-)  A
 371 TYR   ( 402-)  A
 378 TYR   ( 409-)  A
 444 TYR   ( 475-)  A
 575 TYR   (1055-)  B
 585 TYR   (1065-)  B
 611 TYR   (1091-)  B
 643 TYR   (1122-)  B
 655 TYR   (1134-)  B
 783 TYR   (1262-)  B
 869 TYR   (1348-)  B
 894 TYR   (1373-)  B
 923 TYR   (1402-)  B
 930 TYR   (1409-)  B
 996 TYR   (1475-)  B
1127 TYR   (2055-)  C
1137 TYR   (2065-)  C
1163 TYR   (2091-)  C
1195 TYR   (2122-)  C
1207 TYR   (2134-)  C
1335 TYR   (2262-)  C
1421 TYR   (2348-)  C
1446 TYR   (2373-)  C
1475 TYR   (2402-)  C
1482 TYR   (2409-)  C
1548 TYR   (2475-)  C
1679 TYR   (3055-)  D
1689 TYR   (3065-)  D
1715 TYR   (3091-)  D
1747 TYR   (3122-)  D
1759 TYR   (3134-)  D
1887 TYR   (3262-)  D
1973 TYR   (3348-)  D
1998 TYR   (3373-)  D
2027 TYR   (3402-)  D
2034 TYR   (3409-)  D
2100 TYR   (3475-)  D

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
  76 PHE   ( 107-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 189 PHE   ( 220-)  A
 216 PHE   ( 247-)  A
 254 PHE   ( 285-)  A
 298 PHE   ( 329-)  A
 336 PHE   ( 367-)  A
 364 PHE   ( 395-)  A
 439 PHE   ( 470-)  A
 498 PHE   ( 529-)  A
 519 PHE   ( 550-)  A
 546 PHE   ( 577-)  A
 549 PHE   ( 580-)  A
 572 PHE   (1052-)  B
 628 PHE   (1107-)  B
 719 PHE   (1198-)  B
 722 PHE   (1201-)  B
 741 PHE   (1220-)  B
 768 PHE   (1247-)  B
 806 PHE   (1285-)  B
 850 PHE   (1329-)  B
 888 PHE   (1367-)  B
 916 PHE   (1395-)  B
And so on for a total of 61 lines.

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.

  26 ASP   (  58-)  A
 142 ASP   ( 173-)  A
 198 ASP   ( 229-)  A
 208 ASP   ( 239-)  A
 218 ASP   ( 249-)  A
 283 ASP   ( 314-)  A
 362 ASP   ( 393-)  A
 422 ASP   ( 453-)  A
 466 ASP   ( 497-)  A
 578 ASP   (1058-)  B
 694 ASP   (1173-)  B
 750 ASP   (1229-)  B
 760 ASP   (1239-)  B
 770 ASP   (1249-)  B
 835 ASP   (1314-)  B
 914 ASP   (1393-)  B
 974 ASP   (1453-)  B
1018 ASP   (1497-)  B
1130 ASP   (2058-)  C
1246 ASP   (2173-)  C
1302 ASP   (2229-)  C
1312 ASP   (2239-)  C
1322 ASP   (2249-)  C
1387 ASP   (2314-)  C
1466 ASP   (2393-)  C
1526 ASP   (2453-)  C
1570 ASP   (2497-)  C
1682 ASP   (3058-)  D
1798 ASP   (3173-)  D
1854 ASP   (3229-)  D
1864 ASP   (3239-)  D
1874 ASP   (3249-)  D
1939 ASP   (3314-)  D
2018 ASP   (3393-)  D
2078 ASP   (3453-)  D
2122 ASP   (3497-)  D

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.

  14 GLU   (  46-)  A
  41 GLU   (  73-)  A
 109 GLU   ( 140-)  A
 139 GLU   ( 170-)  A
 205 GLU   ( 236-)  A
 259 GLU   ( 290-)  A
 277 GLU   ( 308-)  A
 288 GLU   ( 319-)  A
 295 GLU   ( 326-)  A
 333 GLU   ( 364-)  A
 434 GLU   ( 465-)  A
 453 GLU   ( 484-)  A
 459 GLU   ( 490-)  A
 493 GLU   ( 524-)  A
 566 GLU   (1046-)  B
 593 GLU   (1073-)  B
 661 GLU   (1140-)  B
 691 GLU   (1170-)  B
 757 GLU   (1236-)  B
 781 GLU   (1260-)  B
 811 GLU   (1290-)  B
 829 GLU   (1308-)  B
 840 GLU   (1319-)  B
 847 GLU   (1326-)  B
 885 GLU   (1364-)  B
And so on for a total of 59 lines.

Geometric checks

Warning: Unusual bond angles

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

 117 TYR   ( 148-)  A      N    CA   C    98.86   -4.4
 355 HIS   ( 386-)  A      CG   ND1  CE1 109.62    4.0
 669 TYR   (1148-)  B      N    CA   C    98.48   -4.5
 753 HIS   (1232-)  B      CG   ND1  CE1 109.63    4.0
1221 TYR   (2148-)  C      N    CA   C    98.37   -4.6
1857 HIS   (3232-)  D      CG   ND1  CE1 109.64    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.

  14 GLU   (  46-)  A
  26 ASP   (  58-)  A
  41 GLU   (  73-)  A
 109 GLU   ( 140-)  A
 139 GLU   ( 170-)  A
 142 ASP   ( 173-)  A
 198 ASP   ( 229-)  A
 205 GLU   ( 236-)  A
 208 ASP   ( 239-)  A
 218 ASP   ( 249-)  A
 259 GLU   ( 290-)  A
 277 GLU   ( 308-)  A
 283 ASP   ( 314-)  A
 288 GLU   ( 319-)  A
 295 GLU   ( 326-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 422 ASP   ( 453-)  A
 434 GLU   ( 465-)  A
 453 GLU   ( 484-)  A
 459 GLU   ( 490-)  A
 466 ASP   ( 497-)  A
 493 GLU   ( 524-)  A
 566 GLU   (1046-)  B
 578 ASP   (1058-)  B
And so on for a total of 95 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.

1053 LYS   (1532-)  B    6.34
1605 LYS   (2532-)  C    6.27
2157 LYS   (3532-)  D    6.19
 501 LYS   ( 532-)  A    5.88
1826 PHE   (3201-)  D    5.40
 170 PHE   ( 201-)  A    5.32
1917 PHE   (3292-)  D    5.30
 813 PHE   (1292-)  B    5.27
 261 PHE   ( 292-)  A    5.26
 463 LEU   ( 494-)  A    5.23
1567 LEU   (2494-)  C    5.04
 722 PHE   (1201-)  B    5.01
1221 TYR   (2148-)  C    4.89
 315 GLU   ( 346-)  A    4.85
 669 TYR   (1148-)  B    4.85
1015 LEU   (1494-)  B    4.81
1274 PHE   (2201-)  C    4.81
1375 ALA   (2302-)  C    4.77
 117 TYR   ( 148-)  A    4.71
 867 GLU   (1346-)  B    4.69
2119 LEU   (3494-)  D    4.66
1485 SER   (2412-)  C    4.65
 271 ALA   ( 302-)  A    4.62
1365 PHE   (2292-)  C    4.58
 933 SER   (1412-)  B    4.52
 823 ALA   (1302-)  B    4.51
1270 MET   (2197-)  C    4.49
1971 GLU   (3346-)  D    4.45
1419 GLU   (2346-)  C    4.44
2037 SER   (3412-)  D    4.43
 381 SER   ( 412-)  A    4.34
1822 MET   (3197-)  D    4.17
 462 ALA   ( 493-)  A    4.12
 718 MET   (1197-)  B    4.08
 166 MET   ( 197-)  A    4.06
1060 ILE   (1539-)  B    4.06
1773 TYR   (3148-)  D    4.05

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 : 1.635

Error: Connections to aromatic rings out of plane

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

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

1764 TRP   (3139-)  D      CB   4.02
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -6.019

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 : -6.019

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.

2034 TYR   (3409-)  D    -3.5
 930 TYR   (1409-)  B    -3.5
1482 TYR   (2409-)  C    -3.5
 378 TYR   ( 409-)  A    -3.5
2146 THR   (3521-)  D    -3.5
1594 THR   (2521-)  C    -3.4
 490 THR   ( 521-)  A    -3.4
 928 PHE   (1407-)  B    -3.3
2032 PHE   (3407-)  D    -3.3
 376 PHE   ( 407-)  A    -3.3
1042 THR   (1521-)  B    -3.3
1480 PHE   (2407-)  C    -3.2
  75 PRO   ( 106-)  A    -3.1
1179 PRO   (2106-)  C    -3.1
 627 PRO   (1106-)  B    -3.1
1731 PRO   (3106-)  D    -3.1
1622 THR   (2549-)  C    -2.9
 483 PRO   ( 514-)  A    -2.9
1060 ILE   (1539-)  B    -2.9
1612 ILE   (2539-)  C    -2.9
1587 PRO   (2514-)  C    -2.9
1035 PRO   (1514-)  B    -2.9
2164 ILE   (3539-)  D    -2.9
 508 ILE   ( 539-)  A    -2.8
 518 THR   ( 549-)  A    -2.8
And so on for a total of 290 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.

  12 ARG   (  44-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  33 TYR   (  65-)  A  Poor phi/psi
  37 CYS   (  69-)  A  Poor phi/psi
  50 LEU   (  82-)  A  Poor phi/psi
  63 HIS   (  95-)  A  Poor phi/psi
  72 ASN   ( 104-)  A  Poor phi/psi
  75 PRO   ( 106-)  A  Poor phi/psi
  89 ARG   ( 120-)  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
 110 ALA   ( 141-)  A  Poor phi/psi
 145 GLU   ( 176-)  A  Poor phi/psi
 149 LYS   ( 180-)  A  Poor phi/psi
 150 VAL   ( 181-)  A  Poor phi/psi
 170 PHE   ( 201-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 223 TYR   ( 254-)  A  Poor phi/psi
 239 GLN   ( 270-)  A  Poor phi/psi
 257 GLY   ( 288-)  A  Poor phi/psi
 261 PHE   ( 292-)  A  Poor phi/psi
 271 ALA   ( 302-)  A  Poor phi/psi
 316 ASP   ( 347-)  A  Poor phi/psi
And so on for a total of 196 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -6.564

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.

 972 SER   (1451-)  B    0.37
2076 SER   (3451-)  D    0.37

Warning: Unusual backbone conformations

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

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

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

   5 CYS   (  37-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  12 ARG   (  44-)  A      0
  18 THR   (  50-)  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
  33 TYR   (  65-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  39 THR   (  71-)  A      0
  49 LEU   (  81-)  A      0
  50 LEU   (  82-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  90 SER   ( 121-)  A      0
  92 LEU   ( 123-)  A      0
  94 ASP   ( 125-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
And so on for a total of 884 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 : 1.143

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!

1004 GLY   (1483-)  B   1.90   12
2108 GLY   (3483-)  D   1.88   12
1556 GLY   (2483-)  C   1.83   14
 452 GLY   ( 483-)  A   1.82   14
 511 PRO   ( 542-)  A   1.67   14
1063 PRO   (1542-)  B   1.64   14
1615 PRO   (2542-)  C   1.64   14
2167 PRO   (3542-)  D   1.60   15

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]

 474 PRO   ( 505-)  A    0.20 LOW
1026 PRO   (1505-)  B    0.19 LOW
1578 PRO   (2505-)  C    0.20 LOW
2172 PRO   (3547-)  D    0.20 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].

  40 PRO   (  72-)  A   -50.9 half-chair C-beta/C-alpha (-54 degrees)
  54 PRO   (  86-)  A  -117.0 envelop C-gamma (-108 degrees)
  75 PRO   ( 106-)  A   143.0 envelop C-alpha (144 degrees)
  97 PRO   ( 128-)  A  -142.3 envelop C-delta (-144 degrees)
 131 PRO   ( 162-)  A   102.0 envelop C-beta (108 degrees)
 141 PRO   ( 172-)  A  -135.9 envelop C-delta (-144 degrees)
 160 PRO   ( 191-)  A  -118.6 half-chair C-delta/C-gamma (-126 degrees)
 233 PRO   ( 264-)  A   -19.4 half-chair C-alpha/N (-18 degrees)
 245 PRO   ( 276-)  A   -40.3 envelop C-alpha (-36 degrees)
 246 PRO   ( 277-)  A   128.2 half-chair C-beta/C-alpha (126 degrees)
 358 PRO   ( 389-)  A  -157.0 half-chair N/C-delta (-162 degrees)
 410 PRO   ( 441-)  A   107.3 envelop C-beta (108 degrees)
 481 PRO   ( 512-)  A   110.1 envelop C-beta (108 degrees)
 483 PRO   ( 514-)  A   123.8 half-chair C-beta/C-alpha (126 degrees)
 507 PRO   ( 538-)  A  -137.7 envelop C-delta (-144 degrees)
 516 PRO   ( 547-)  A  -169.3 half-chair N/C-delta (-162 degrees)
 592 PRO   (1072-)  B   -53.5 half-chair C-beta/C-alpha (-54 degrees)
 606 PRO   (1086-)  B  -116.9 envelop C-gamma (-108 degrees)
 627 PRO   (1106-)  B   138.1 envelop C-alpha (144 degrees)
 649 PRO   (1128-)  B  -139.1 envelop C-delta (-144 degrees)
 683 PRO   (1162-)  B   101.8 envelop C-beta (108 degrees)
 693 PRO   (1172-)  B  -136.4 envelop C-delta (-144 degrees)
 712 PRO   (1191-)  B  -115.3 envelop C-gamma (-108 degrees)
 739 PRO   (1218-)  B    51.6 half-chair C-delta/C-gamma (54 degrees)
 785 PRO   (1264-)  B   -17.0 half-chair C-alpha/N (-18 degrees)
And so on for a total of 66 lines.

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.

1596 VAL   (2523-)  C      CG1 <-> 2236 BOG   (2701-)  C      C8'    1.70    0.60  INTRA BL
1596 VAL   (2523-)  C      CG1 <-> 2236 BOG   (2701-)  C      C7'    1.27    1.53  INTRA BL
1596 VAL   (2523-)  C      CG1 <-> 2236 BOG   (2701-)  C      C6'    1.08    2.12  INTRA BL
1596 VAL   (2523-)  C      CB  <-> 2236 BOG   (2701-)  C      C7'    1.07    1.23  INTRA BL
1596 VAL   (2523-)  C      C   <-> 2236 BOG   (2701-)  C      C7'    0.96    1.34  INTRA BL
1282 PHE   (2209-)  C      CE2 <-> 2236 BOG   (2701-)  C      O4     0.82    1.98  INTRA
1278 PHE   (2205-)  C      CD2 <-> 2236 BOG   (2701-)  C      O3     0.82    1.98  INTRA
1596 VAL   (2523-)  C      CG2 <-> 2236 BOG   (2701-)  C      C6'    0.75    2.45  INTRA BL
1596 VAL   (2523-)  C      CB  <-> 2236 BOG   (2701-)  C      C6'    0.69    2.11  INTRA BL
1454 PHE   (2381-)  C      CZ  <-> 2236 BOG   (2701-)  C      C6     0.67    2.13  INTRA B3
1279 THR   (2206-)  C      CG2 <-> 2236 BOG   (2701-)  C      O4     0.64    2.16  INTRA BL
1282 PHE   (2209-)  C      CZ  <-> 2236 BOG   (2701-)  C      O4     0.60    2.20  INTRA
1596 VAL   (2523-)  C      C   <-> 2236 BOG   (2701-)  C      C5'    0.57    2.63  INTRA BL
1597 GLU   (2524-)  C      N   <-> 2236 BOG   (2701-)  C      C7'    0.55    2.15  INTRA BL
1596 VAL   (2523-)  C      C   <-> 2236 BOG   (2701-)  C      C6'    0.54    2.26  INTRA BL
1596 VAL   (2523-)  C      O   <-> 2236 BOG   (2701-)  C      C5'    0.53    2.27  INTRA BL
1596 VAL   (2523-)  C      O   <-> 2236 BOG   (2701-)  C      C6'    0.53    2.27  INTRA BL
1279 THR   (2206-)  C      CG2 <-> 2236 BOG   (2701-)  C      C3     0.50    2.70  INTRA BL
1596 VAL   (2523-)  C      CA  <-> 2236 BOG   (2701-)  C      C5'    0.50    2.30  INTRA BL
1597 GLU   (2524-)  C      N   <-> 2236 BOG   (2701-)  C      C8'    0.46    2.64  INTRA BL
1833 GLN   (3208-)  D      NE2 <-> 1857 HIS   (3232-)  D      NE2    0.45    2.55  INTRA BL
 354 TYR   ( 385-)  A      O   <->  356 TRP   ( 387-)  A      N      0.45    2.25  INTRA
1281 GLN   (2208-)  C      NE2 <-> 1305 HIS   (2232-)  C      NE2    0.44    2.56  INTRA BL
2010 TYR   (3385-)  D      O   <-> 2012 TRP   (3387-)  D      N      0.44    2.26  INTRA
 177 GLN   ( 208-)  A      NE2 <->  201 HIS   ( 232-)  A      NE2    0.44    2.56  INTRA BL
And so on for a total of 1968 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

  29 ARG   (  61-)  A      -6.94
 581 ARG   (1061-)  B      -6.92
1133 ARG   (2061-)  C      -6.91
1685 ARG   (3061-)  D      -6.87
 799 HIS   (1278-)  B      -6.83
 247 HIS   ( 278-)  A      -6.83
1903 HIS   (3278-)  D      -6.82
1351 HIS   (2278-)  C      -6.82
 138 LYS   ( 169-)  A      -6.24
 690 LYS   (1169-)  B      -6.23
1242 LYS   (2169-)  C      -6.23
1794 LYS   (3169-)  D      -6.21
 938 HIS   (1417-)  B      -5.72
2042 HIS   (3417-)  D      -5.72
1490 HIS   (2417-)  C      -5.70
 386 HIS   ( 417-)  A      -5.68
1327 TYR   (2254-)  C      -5.62
1616 GLN   (2543-)  C      -5.54
2168 GLN   (3543-)  D      -5.52
 223 TYR   ( 254-)  A      -5.51
1900 TYR   (3275-)  D      -5.46
 737 ARG   (1216-)  B      -5.44
1348 TYR   (2275-)  C      -5.43
1064 GLN   (1543-)  B      -5.42
1841 ARG   (3216-)  D      -5.42
 775 TYR   (1254-)  B      -5.42
 244 TYR   ( 275-)  A      -5.40
 796 TYR   (1275-)  B      -5.40
2202 PHE   (3577-)  D      -5.39
1879 TYR   (3254-)  D      -5.39
 512 GLN   ( 543-)  A      -5.38
 185 ARG   ( 216-)  A      -5.36
1650 PHE   (2577-)  C      -5.36
 184 LYS   ( 215-)  A      -5.33
1098 PHE   (1577-)  B      -5.31
1289 ARG   (2216-)  C      -5.24
 736 LYS   (1215-)  B      -5.21
1840 LYS   (3215-)  D      -5.20
1288 LYS   (2215-)  C      -5.19
1644 ASN   (2571-)  C      -5.05
 139 GLU   ( 170-)  A      -5.04
 540 ASN   ( 571-)  A      -5.04
2196 ASN   (3571-)  D      -5.04
1092 ASN   (1571-)  B      -5.03
1944 GLU   (3319-)  D      -5.01
1392 GLU   (2319-)  C      -5.01
 288 GLU   ( 319-)  A      -5.01
 840 GLU   (1319-)  B      -5.00

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.

  20 PHE   (  52-)  A        22 - GLN     54- ( A)         -4.43
 572 PHE   (1052-)  B       574 - GLN   1054- ( B)         -4.49
1124 PHE   (2052-)  C      1126 - GLN   2054- ( C)         -4.48
1676 PHE   (3052-)  D      1678 - GLN   3054- ( D)         -4.44

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 2224 : -1.415

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

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: D

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.

 898 ILE   (1377-)  B   -2.51

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

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

2237 HOH   (4001 )  A      O
2237 HOH   (4018 )  A      O
2237 HOH   (4020 )  A      O
2238 HOH   (4073 )  B      O
2239 HOH   (4114 )  C      O
2239 HOH   (4116 )  C      O
2240 HOH   (4163 )  D      O
Bound group on Asn; dont flip   36 ASN  (  68-) A
Bound to: 2209 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 2211 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 2212 NAG  ( 681-) A
Bound group on Asn; dont flip  588 ASN  (1068-) B
Bound to: 2213 NAG  (1661-) B
Bound group on Asn; dont flip  665 ASN  (1144-) B
Bound to: 2215 NAG  (1671-) B
Bound group on Asn; dont flip  931 ASN  (1410-) B
Bound to: 2216 NAG  (1681-) B
Bound group on Asn; dont flip 1140 ASN  (2068-) C
Bound to: 2217 NAG  (2661-) C
Bound group on Asn; dont flip 1217 ASN  (2144-) C
Bound to: 2219 NAG  (2671-) C
Bound group on Asn; dont flip 1483 ASN  (2410-) C
Bound to: 2220 NAG  (2681-) C
Bound group on Asn; dont flip 1692 ASN  (3068-) D
Bound to: 2221 NAG  (3661-) D
Bound group on Asn; dont flip 1769 ASN  (3144-) D
Bound to: 2223 NAG  (3671-) D
Bound group on Asn; dont flip 2035 ASN  (3410-) D
Bound to: 2224 NAG  (3681-) D

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.

 176 HIS   ( 207-)  A
 357 HIS   ( 388-)  A
 423 GLN   ( 454-)  A
 433 ASN   ( 464-)  A
 728 HIS   (1207-)  B
 877 HIS   (1356-)  B
 909 HIS   (1388-)  B
 975 GLN   (1454-)  B
 985 ASN   (1464-)  B
1280 HIS   (2207-)  C
1461 HIS   (2388-)  C
1527 GLN   (2454-)  C
1537 ASN   (2464-)  C
1832 HIS   (3207-)  D
1857 HIS   (3232-)  D
2013 HIS   (3388-)  D
2079 GLN   (3454-)  D
2089 ASN   (3464-)  D

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   9 CYS   (  41-)  A      N
  14 GLU   (  46-)  A      N
  36 ASN   (  68-)  A      N
  45 ARG   (  77-)  A      NE
  98 THR   ( 129-)  A      N
 105 TYR   ( 136-)  A      N
 106 LYS   ( 137-)  A      NZ
 107 SER   ( 138-)  A      N
 107 SER   ( 138-)  A      OG
 114 LEU   ( 145-)  A      N
 116 TYR   ( 147-)  A      N
 117 TYR   ( 148-)  A      OH
 135 LYS   ( 166-)  A      N
 178 PHE   ( 209-)  A      N
 191 ARG   ( 222-)  A      N
 191 ARG   ( 222-)  A      NE
 201 HIS   ( 232-)  A      N
 201 HIS   ( 232-)  A      ND1
 214 ARG   ( 245-)  A      NE
 214 ARG   ( 245-)  A      NH1
 214 ARG   ( 245-)  A      NH2
 216 PHE   ( 247-)  A      N
 224 GLN   ( 255-)  A      NE2
 234 THR   ( 265-)  A      N
 256 VAL   ( 287-)  A      N
And so on for a total of 228 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.

 109 GLU   ( 140-)  A      OE2
 201 HIS   ( 232-)  A      NE2
 211 HIS   ( 242-)  A      ND1
 289 HIS   ( 320-)  A      NE2
 308 GLU   ( 339-)  A      OE1
 319 GLN   ( 350-)  A      OE1
 390 GLN   ( 421-)  A      OE1
 471 GLU   ( 502-)  A      OE2
 493 GLU   ( 524-)  A      OE1
 661 GLU   (1140-)  B      OE2
 753 HIS   (1232-)  B      NE2
 763 HIS   (1242-)  B      ND1
 789 ASP   (1268-)  B      OD1
 841 HIS   (1320-)  B      NE2
 847 GLU   (1326-)  B      OE1
 860 GLU   (1339-)  B      OE1
 942 GLN   (1421-)  B      OE1
1023 GLU   (1502-)  B      OE2
1213 GLU   (2140-)  C      OE2
1315 HIS   (2242-)  C      ND1
1393 HIS   (2320-)  C      NE2
1412 GLU   (2339-)  C      OE1
1423 GLN   (2350-)  C      OE1
1575 GLU   (2502-)  C      OE2
1765 GLU   (3140-)  D      OE2
1815 ASP   (3190-)  D      OD1
1867 HIS   (3242-)  D      ND1
1893 ASP   (3268-)  D      OD1
1945 HIS   (3320-)  D      NE2
1947 GLU   (3322-)  D      OE1
1964 GLU   (3339-)  D      OE1
2046 GLN   (3421-)  D      OE1
2127 GLU   (3502-)  D      OE2
2149 GLU   (3524-)  D      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.

  21 ASP   (  53-)  A   H-bonding suggests Asn; but Alt-Rotamer
 218 ASP   ( 249-)  A   H-bonding suggests Asn
 229 GLU   ( 260-)  A   H-bonding suggests Gln; but Alt-Rotamer
 237 ASP   ( 268-)  A   H-bonding suggests Asn
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 422 ASP   ( 453-)  A   H-bonding suggests Asn
 484 ASP   ( 515-)  A   H-bonding suggests Asn
 573 ASP   (1053-)  B   H-bonding suggests Asn
 757 GLU   (1236-)  B   H-bonding suggests Gln; but Alt-Rotamer
 770 ASP   (1249-)  B   H-bonding suggests Asn
 781 GLU   (1260-)  B   H-bonding suggests Gln
 789 ASP   (1268-)  B   H-bonding suggests Asn
 843 GLU   (1322-)  B   H-bonding suggests Gln
 974 ASP   (1453-)  B   H-bonding suggests Asn; but Alt-Rotamer
1036 ASP   (1515-)  B   H-bonding suggests Asn
1125 ASP   (2053-)  C   H-bonding suggests Asn; but Alt-Rotamer
1309 GLU   (2236-)  C   H-bonding suggests Gln; but Alt-Rotamer
1322 ASP   (2249-)  C   H-bonding suggests Asn
1333 GLU   (2260-)  C   H-bonding suggests Gln
1341 ASP   (2268-)  C   H-bonding suggests Asn
1395 GLU   (2322-)  C   H-bonding suggests Gln
1526 ASP   (2453-)  C   H-bonding suggests Asn
1588 ASP   (2515-)  C   H-bonding suggests Asn
1677 ASP   (3053-)  D   H-bonding suggests Asn
1874 ASP   (3249-)  D   H-bonding suggests Asn
1885 GLU   (3260-)  D   H-bonding suggests Gln
1893 ASP   (3268-)  D   H-bonding suggests Asn
1947 GLU   (3322-)  D   H-bonding suggests Gln
2078 ASP   (3453-)  D   H-bonding suggests Asn; but Alt-Rotamer
2140 ASP   (3515-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.287
  2nd generation packing quality :  -2.404
  Ramachandran plot appearance   :  -6.019 (bad)
  chi-1/chi-2 rotamer normality  :  -6.564 (bad)
  Backbone conformation          :  -1.200

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.371 (tight)
  Bond angles                    :   0.642 (tight)
  Omega angle restraints         :   0.208 (tight)
  Side chain planarity           :   0.161 (tight)
  Improper dihedral distribution :   0.615
  B-factor distribution          :   1.273
  Inside/Outside distribution    :   1.106

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.2
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -3.3 (poor)
  chi-1/chi-2 rotamer normality  :  -4.0 (poor)
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.371 (tight)
  Bond angles                    :   0.642 (tight)
  Omega angle restraints         :   0.208 (tight)
  Side chain planarity           :   0.161 (tight)
  Improper dihedral distribution :   0.615
  B-factor distribution          :   1.273
  Inside/Outside distribution    :   1.106
==============

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.