WHAT IF Check report

This file was created 2013-01-17 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 pdb3i4m.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 2 2 21
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 461573.156
Volume of the Unit Cell V= 24344700.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 13.186
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 5.720 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

2901 ASP   ( 111-)  D      CG
2901 ASP   ( 111-)  D      OD1
2901 ASP   ( 111-)  D      OD2
2902 ASP   ( 112-)  D      CG
2902 ASP   ( 112-)  D      OD1
2902 ASP   ( 112-)  D      OD2

Warning: B-factors outside the range 0.0 - 100.0

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

   1 VAL   (   2-)  A    High
   2 GLY   (   3-)  A    High
   4 GLN   (   5-)  A    High
  38 GLU   (  39-)  A    High
  40 MET   (  41-)  A    High
  41 ASP   (  42-)  A    High
  42 GLU   (  43-)  A    High
  43 THR   (  44-)  A    High
  44 GLN   (  45-)  A    High
  45 THR   (  46-)  A    High
  46 ARG   (  47-)  A    High
  61 ASP   (  62-)  A    High
  62 ARG   (  63-)  A    High
  65 LYS   (  66-)  A    High
  67 GLN   (  68-)  A    High
  68 THR   (  69-)  A    High
  69 CYS   (  70-)  A    High
  70 GLN   (  71-)  A    High
 105 VAL   ( 106-)  A    High
 106 CYS   ( 107-)  A    High
 107 MET   ( 108-)  A    High
 108 HIS   ( 109-)  A    High
 109 CYS   ( 110-)  A    High
 110 GLY   ( 111-)  A    High
 111 LYS   ( 112-)  A    High
And so on for a total of 1443 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

2836 ARG   (  12-)  D
2837 ARG   (  13-)  D

Warning: Tyrosine convention problem

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

 382 TYR   ( 383-)  A
 403 TYR   ( 404-)  A
 477 TYR   ( 478-)  A
 803 TYR   ( 804-)  A
 851 TYR   ( 852-)  A
 932 TYR   ( 933-)  A
1107 TYR   (1119-)  A
1261 TYR   (1287-)  A
1323 TYR   (1349-)  A
1339 TYR   (1365-)  A
1427 TYR   (1453-)  A
1669 TYR   ( 303-)  B
1817 TYR   ( 459-)  B
1844 TYR   ( 486-)  B
1992 TYR   ( 634-)  B
2041 TYR   ( 692-)  B
2128 TYR   ( 785-)  B
2141 TYR   ( 798-)  B
2324 TYR   ( 994-)  B
2394 TYR   (1064-)  B
2422 TYR   (1092-)  B
2528 TYR   (1198-)  B
3178 TYR   ( 168-)  E
3221 TYR   ( 211-)  E
3364 TYR   (  51-)  G
3387 TYR   (  74-)  G
3504 TYR   (  20-)  H
3570 TYR   (  95-)  H
3577 TYR   ( 102-)  H
3654 TYR   (  34-)  I
3781 TYR   (  44-)  J
3800 TYR   (  63-)  J
3863 TYR   (  61-)  K
3883 TYR   (  81-)  K
3924 TYR   (  29-)  L

Warning: Phenylalanine convention problem

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

  18 PHE   (  19-)  A
  21 PHE   (  22-)  A
  94 PHE   (  95-)  A
 218 PHE   ( 219-)  A
 227 PHE   ( 228-)  A
 251 PHE   ( 252-)  A
 263 PHE   ( 264-)  A
 467 PHE   ( 468-)  A
 481 PHE   ( 482-)  A
 590 PHE   ( 591-)  A
 720 PHE   ( 721-)  A
 776 PHE   ( 777-)  A
 778 PHE   ( 779-)  A
 786 PHE   ( 787-)  A
 813 PHE   ( 814-)  A
 814 PHE   ( 815-)  A
 865 PHE   ( 866-)  A
 892 PHE   ( 893-)  A
 941 PHE   ( 942-)  A
1041 PHE   (1042-)  A
1052 PHE   (1053-)  A
1306 PHE   (1332-)  A
1384 PHE   (1410-)  A
1448 PHE   (  38-)  B
1520 PHE   ( 129-)  B
And so on for a total of 57 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.

 194 ASP   ( 195-)  A
 260 ASP   ( 261-)  A
 361 ASP   ( 362-)  A
 480 ASP   ( 481-)  A
 780 ASP   ( 781-)  A
1420 ASP   (1446-)  A
1660 ASP   ( 294-)  B
2026 ASP   ( 668-)  B
2043 ASP   ( 694-)  B
2133 ASP   ( 790-)  B
2234 ASP   ( 891-)  B
2917 ASP   ( 127-)  D
3401 ASP   (  88-)  G

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.

 332 GLU   ( 333-)  A
 495 GLU   ( 496-)  A
 677 GLU   ( 678-)  A
 800 GLU   ( 801-)  A
 878 GLU   ( 879-)  A
1378 GLU   (1404-)  A
1438 GLU   (  28-)  B
1475 GLU   (  65-)  B
1552 GLU   ( 186-)  B
2027 GLU   ( 678-)  B
2048 GLU   ( 699-)  B
2358 GLU   (1028-)  B
2400 GLU   (1070-)  B
2464 GLU   (1134-)  B
2606 GLU   (  52-)  C
2762 GLU   ( 208-)  C
2878 GLU   (  54-)  D
3008 GLU   ( 218-)  D
3147 GLU   ( 137-)  E
3272 GLU   ( 114-)  F
3447 GLU   ( 134-)  G
3702 GLU   (  82-)  I
3756 GLU   (  19-)  J
3866 GLU   (  64-)  K

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.

3986 DCYT  (  27-)  T      C1'  N1    1.57    8.0

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.000392  0.000064 -0.000043|
 |  0.000064  1.000600 -0.000180|
 | -0.000043 -0.000180  1.000313|
Proposed new scale matrix

 |  0.004530  0.000000  0.000000|
 |  0.000000  0.002549  0.000000|
 |  0.000000  0.000000  0.003552|
With corresponding cell

    A    = 220.740  B   = 392.238  C    = 281.540
    Alpha=  90.004  Beta=  90.003  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 220.646  B   = 392.003  C    = 281.455
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 30.398
(Under-)estimated Z-score: 4.063

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.

   2 GLY   (   3-)  A      N    CA   C    98.73   -4.7
 310 GLN   ( 311-)  A      N    CA   C   123.47    4.4
 343 ARG   ( 344-)  A      N    CA   C    98.70   -4.5
 439 ASP   ( 440-)  A      N    CA   C    97.77   -4.8
 460 LYS   ( 461-)  A      N    CA   C    99.26   -4.3
1673 ASP   ( 307-)  B      N    CA   C    98.98   -4.4
1690 ILE   ( 324-)  B      N    CA   C    99.41   -4.2
1756 LEU   ( 390-)  B      N    CA   C    99.06   -4.3
2087 HIS   ( 744-)  B      CG   ND1  CE1 109.71    4.1
2225 THR   ( 882-)  B      N    CA   C   122.92    4.2
2426 ARG   (1096-)  B      N    CA   C    98.39   -4.6
2493 CYS   (1163-)  B      N    CA   C    98.19   -4.6
2525 HIS   (1195-)  B      CG   ND1  CE1 109.62    4.0
2593 ALA   (  39-)  C      N    CA   C   123.35    4.3
2727 ALA   ( 173-)  C      N    CA   C   122.46    4.0
2904 MET   ( 114-)  D      N    CA   C   122.93    4.2
3015 ASN   (   5-)  E      N    CA   C    99.32   -4.2
3358 ILE   (  45-)  G      N    CA   C    99.89   -4.0
3971 DGUA  (  12-)  T      N9   C8   N7  113.27    4.3
3979 DGUA  (  20-)  T      N9   C8   N7  113.29    4.4
3980 DCYT  (  21-)  T      O4'  C1'  N1  111.01    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.

 194 ASP   ( 195-)  A
 260 ASP   ( 261-)  A
 332 GLU   ( 333-)  A
 361 ASP   ( 362-)  A
 480 ASP   ( 481-)  A
 495 GLU   ( 496-)  A
 677 GLU   ( 678-)  A
 780 ASP   ( 781-)  A
 800 GLU   ( 801-)  A
 878 GLU   ( 879-)  A
1378 GLU   (1404-)  A
1420 ASP   (1446-)  A
1438 GLU   (  28-)  B
1475 GLU   (  65-)  B
1552 GLU   ( 186-)  B
1660 ASP   ( 294-)  B
2026 ASP   ( 668-)  B
2027 GLU   ( 678-)  B
2043 ASP   ( 694-)  B
2048 GLU   ( 699-)  B
2133 ASP   ( 790-)  B
2234 ASP   ( 891-)  B
2358 GLU   (1028-)  B
2400 GLU   (1070-)  B
2464 GLU   (1134-)  B
2606 GLU   (  52-)  C
2762 GLU   ( 208-)  C
2836 ARG   (  12-)  D
2837 ARG   (  13-)  D
2878 GLU   (  54-)  D
2917 ASP   ( 127-)  D
3008 GLU   ( 218-)  D
3147 GLU   ( 137-)  E
3272 GLU   ( 114-)  F
3401 ASP   (  88-)  G
3447 GLU   ( 134-)  G
3702 GLU   (  82-)  I
3756 GLU   (  19-)  J
3866 GLU   (  64-)  K

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

1102 PRO   (1114-)  A      N     -6.0   -22.21    -2.48
The average deviation= 0.803

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.

2593 ALA   (  39-)  C    8.27
3015 ASN   (   5-)  E    7.23
 709 LEU   ( 710-)  A    7.15
 453 SER   ( 454-)  A    7.08
2978 ALA   ( 188-)  D    7.08
 688 LYS   ( 689-)  A    6.76
1085 GLY   (1097-)  A    5.88
3187 ARG   ( 177-)  E    5.47
 638 PRO   ( 639-)  A    5.40
 628 LEU   ( 629-)  A    5.34
   2 GLY   (   3-)  A    5.33
 451 LYS   ( 452-)  A    5.32
3781 TYR   (  44-)  J    5.29
3277 ARG   ( 119-)  F    5.26
2383 GLU   (1053-)  B    5.20
2355 HIS   (1025-)  B    5.20
2030 TRP   ( 681-)  B    5.20
1749 ASN   ( 383-)  B    5.03
2430 ASP   (1100-)  B    4.96
1756 LEU   ( 390-)  B    4.95
2535 GLN   (1205-)  B    4.93
1663 ILE   ( 297-)  B    4.92
2426 ARG   (1096-)  B    4.84
2493 CYS   (1163-)  B    4.81
1236 LYS   (1262-)  A    4.79
And so on for a total of 77 lines.

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 : 1.604

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 : -6.532

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.

3843 THR   (  41-)  K    -3.5
3706 PHE   (  86-)  I    -3.4
1015 THR   (1016-)  A    -3.4
2173 TYR   ( 830-)  B    -3.4
 218 PHE   ( 219-)  A    -3.3
1379 THR   (1405-)  A    -3.3
 754 PHE   ( 755-)  A    -3.2
2225 THR   ( 882-)  B    -3.2
3577 TYR   ( 102-)  H    -3.2
3863 TYR   (  61-)  K    -3.2
2903 PHE   ( 113-)  D    -3.2
1110 PRO   (1122-)  A    -3.1
 311 PRO   ( 312-)  A    -3.1
2376 PRO   (1046-)  B    -3.1
3501 PRO   (  17-)  H    -3.1
2544 PRO   (1214-)  B    -3.0
 243 PRO   ( 244-)  A    -3.0
3434 PHE   ( 121-)  G    -3.0
1112 HIS   (1124-)  A    -3.0
  95 ILE   (  96-)  A    -3.0
3741 PRO   (   4-)  J    -3.0
3556 PRO   (  81-)  H    -2.9
 778 PHE   ( 779-)  A    -2.9
2378 THR   (1048-)  B    -2.9
3387 TYR   (  74-)  G    -2.9
And so on for a total of 320 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.

   3 GLN   (   4-)  A  Poor phi/psi
   4 GLN   (   5-)  A  Poor phi/psi
   7 SER   (   8-)  A  Poor phi/psi
  40 MET   (  41-)  A  Poor phi/psi
  41 ASP   (  42-)  A  Poor phi/psi
  42 GLU   (  43-)  A  Poor phi/psi
  44 GLN   (  45-)  A  Poor phi/psi
  47 ALA   (  48-)  A  Poor phi/psi
  50 GLY   (  51-)  A  Poor phi/psi
  54 ASP   (  55-)  A  Poor phi/psi
  56 ARG   (  57-)  A  Poor phi/psi
  57 LEU   (  58-)  A  Poor phi/psi
  58 GLY   (  59-)  A  Poor phi/psi
  61 ASP   (  62-)  A  Poor phi/psi
  62 ARG   (  63-)  A  Poor phi/psi
  66 CYS   (  67-)  A  Poor phi/psi
  68 THR   (  69-)  A  Poor phi/psi
  69 CYS   (  70-)  A  Poor phi/psi
  70 GLN   (  71-)  A  Poor phi/psi
  71 GLU   (  72-)  A  Poor phi/psi
  72 GLY   (  73-)  A  Poor phi/psi
  73 MET   (  74-)  A  Poor phi/psi
  75 GLU   (  76-)  A  Poor phi/psi
 108 HIS   ( 109-)  A  Poor phi/psi
 125 LEU   ( 126-)  A  Poor phi/psi
And so on for a total of 575 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 : -4.596

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.

1848 SER   ( 490-)  B    0.33
1070 SER   (1071-)  A    0.35
1046 SER   (1047-)  A    0.35
3005 SER   ( 215-)  D    0.36
1279 VAL   (1305-)  A    0.36
2762 GLU   ( 208-)  C    0.36
2586 SER   (  32-)  C    0.37
3044 GLU   (  34-)  E    0.38
 916 SER   ( 917-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   3 GLN   (   4-)  A      0
   4 GLN   (   5-)  A      0
   5 TYR   (   6-)  A      0
  33 LYS   (  34-)  A      0
  34 ILE   (  35-)  A      0
  35 ARG   (  36-)  A      0
  36 PHE   (  37-)  A      0
  37 PRO   (  38-)  A      0
  39 THR   (  40-)  A      0
  40 MET   (  41-)  A      0
  41 ASP   (  42-)  A      0
  42 GLU   (  43-)  A      0
  43 THR   (  44-)  A      0
  44 GLN   (  45-)  A      0
  46 ARG   (  47-)  A      0
  47 ALA   (  48-)  A      0
  48 LYS   (  49-)  A      0
  49 ILE   (  50-)  A      0
  52 LEU   (  53-)  A      0
  53 ASN   (  54-)  A      0
  54 ASP   (  55-)  A      0
  55 PRO   (  56-)  A      0
  56 ARG   (  57-)  A      0
  57 LEU   (  58-)  A      0
  60 ILE   (  61-)  A      0
And so on for a total of 1933 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 : 1.129

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!

3502 GLY   (  18-)  H   3.35   13
3815 GLY   (  13-)  K   3.07   16
3602 GLY   ( 127-)  H   2.91   10
3594 GLY   ( 119-)  H   2.77   10
3677 GLY   (  57-)  I   2.23   10
1701 GLY   ( 335-)  B   2.13   17
3947 GLY   (  52-)  L   2.07   12
 672 GLY   ( 673-)  A   2.05   12
1270 GLY   (1296-)  A   2.00   28
2122 GLY   ( 779-)  B   2.00   22
3761 LEU   (  24-)  J   1.88   12
2335 GLY   (1005-)  B   1.83   80
2921 GLU   ( 131-)  D   1.65   28
 573 GLY   ( 574-)  A   1.64   10
1573 GLY   ( 207-)  B   1.64   80
 806 GLY   ( 807-)  A   1.63   19
2797 VAL   ( 243-)  C   1.61   80
2277 GLY   ( 947-)  B   1.61   19
1314 GLY   (1340-)  A   1.58   25
 614 GLY   ( 615-)  A   1.56   16

Warning: Unusual peptide bond conformations

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

1165 LEU   (1177-)  A   1.95
2903 PHE   ( 113-)  D   1.61

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]

  55 PRO   (  56-)  A    0.45 HIGH
  77 PRO   (  78-)  A    0.45 HIGH
 171 PRO   ( 172-)  A    0.45 HIGH
 244 PRO   ( 245-)  A    0.48 HIGH
 247 PRO   ( 248-)  A    0.47 HIGH
 320 PRO   ( 321-)  A    0.45 HIGH
 491 PRO   ( 492-)  A    0.46 HIGH
 513 PRO   ( 514-)  A    0.47 HIGH
 977 PRO   ( 978-)  A    0.45 HIGH
2767 PRO   ( 213-)  C    0.45 HIGH
3297 PRO   ( 139-)  F    0.46 HIGH
3376 PRO   (  63-)  G    0.47 HIGH
3394 PRO   (  81-)  G    0.45 HIGH

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].

 243 PRO   ( 244-)  A  -121.7 half-chair C-delta/C-gamma (-126 degrees)
 311 PRO   ( 312-)  A   109.3 envelop C-beta (108 degrees)
 567 PRO   ( 568-)  A    40.3 envelop C-delta (36 degrees)
1110 PRO   (1122-)  A   107.3 envelop C-beta (108 degrees)
1226 PRO   (1245-)  A   -65.1 envelop C-beta (-72 degrees)
1491 PRO   ( 100-)  B   103.7 envelop C-beta (108 degrees)
1537 PRO   ( 171-)  B  -114.1 envelop C-gamma (-108 degrees)
2142 PRO   ( 799-)  B    50.9 half-chair C-delta/C-gamma (54 degrees)
3556 PRO   (  81-)  H    44.2 envelop C-delta (36 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.

1479 LEU   (  69-)  B      CD1 <-> 1795 PHE   ( 429-)  B      CD1    0.90    2.30  INTRA BF
1479 LEU   (  69-)  B      CD1 <-> 1795 PHE   ( 429-)  B      CE1    0.75    2.45  INTRA BF
3314 MET   (   1-)  G      SD  <-> 3315 PHE   (   2-)  G      N      0.68    2.52  INTRA BL
 664 GLY   ( 665-)  A      O   <->  666 GLY   ( 667-)  A      N      0.64    2.06  INTRA BL
  41 ASP   (  42-)  A      O   <->   43 THR   (  44-)  A      N      0.59    2.11  INTRA BF
3946 CYS   (  51-)  L      CB  <-> 4021  ZN   (1071-)  L     ZN      0.58    2.62  INTRA BF
  68 THR   (  69-)  A      O   <->   70 GLN   (  71-)  A      N      0.57    2.13  INTRA BF
 224 ASN   ( 225-)  A      ND2 <->  227 PHE   ( 228-)  A      N      0.54    2.31  INTRA BL
1660 ASP   ( 294-)  B      O   <-> 1662 GLU   ( 296-)  B      N      0.53    2.17  INTRA BL
1479 LEU   (  69-)  B      CG  <-> 1795 PHE   ( 429-)  B      CE1    0.51    2.69  INTRA BF
2186 GLN   ( 843-)  B      N   <-> 2324 TYR   ( 994-)  B      O      0.51    2.19  INTRA BL
2642 CYS   (  88-)  C      SG  <-> 2645 HIS   (  91-)  C      C      0.50    2.90  INTRA BL
2287 ASN   ( 957-)  B      O   <-> 2289 ASP   ( 959-)  B      N      0.50    2.20  INTRA BF
  33 LYS   (  34-)  A      NZ  <->   56 ARG   (  57-)  A      NH2    0.50    2.35  INTRA BL
3548 ASN   (  64-)  H      OD1 <-> 3565 ALA   (  90-)  H      N      0.50    2.20  INTRA BF
  40 MET   (  41-)  A      SD  <->   41 ASP   (  42-)  A      N      0.49    2.71  INTRA BF
3738 MET   (   1-)  J      N   <-> 3793 LEU   (  56-)  J      N      0.49    2.36  INTRA BL
3548 ASN   (  64-)  H      ND2 <-> 3563 SER   (  88-)  H      C      0.49    2.61  INTRA BF
3237 ARG   (  79-)  F      NH2 <-> 3308 GLU   ( 150-)  F      OE1    0.48    2.22  INTRA BL
3314 MET   (   1-)  G      SD  <-> 3392 PHE   (  79-)  G      CD1    0.47    2.93  INTRA BL
  49 ILE   (  50-)  A      O   <->   51 GLY   (  52-)  A      N      0.47    2.23  INTRA BL
2661 SER   ( 107-)  C      O   <-> 2663 SER   ( 109-)  C      N      0.47    2.23  INTRA BF
2790 GLY   ( 236-)  C      O   <-> 2792 ILE   ( 238-)  C      N      0.47    2.23  INTRA BL
3451 THR   ( 138-)  G      CG2 <-> 3452 ILE   ( 139-)  G      N      0.47    2.53  INTRA BF
2864 HIS   (  40-)  D      CB  <-> 3386 LYS   (  73-)  G      NZ     0.47    2.63  INTRA BF
And so on for a total of 3155 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

1225 ARG   (1244-)  A      -8.00
1862 ARG   ( 504-)  B      -7.90
2903 PHE   ( 113-)  D      -7.75
1949 ARG   ( 591-)  B      -7.41
2904 MET   ( 114-)  D      -7.21
3937 ARG   (  42-)  L      -7.20
3552 ARG   (  77-)  H      -6.97
2004 LEU   ( 646-)  B      -6.96
3555 ARG   (  80-)  H      -6.81
2426 ARG   (1096-)  B      -6.72
1002 LYS   (1003-)  A      -6.68
3010 LEU   ( 220-)  D      -6.57
3628 ARG   (   8-)  I      -6.57
 280 HIS   ( 281-)  A      -6.50
2838 ARG   (  14-)  D      -6.49
 310 GLN   ( 311-)  A      -6.46
  46 ARG   (  47-)  A      -6.44
1707 LEU   ( 341-)  B      -6.40
  35 ARG   (  36-)  A      -6.38
1147 ARG   (1159-)  A      -6.36
2438 ARG   (1108-)  B      -6.35
1360 ARG   (1386-)  A      -6.32
  62 ARG   (  63-)  A      -6.29
 316 LYS   ( 317-)  A      -6.27
   3 GLN   (   4-)  A      -6.24
And so on for a total of 134 lines.

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.

   3 GLN   (   4-)  A         5 - TYR      6- ( A)         -5.36
1449 ARG   (  39-)  B      1451 - LYS     41- ( B)         -4.93
1925 GLU   ( 567-)  B      1927 - TYR    569- ( B)         -4.28
2072 ILE   ( 729-)  B      2074 - VAL    731- ( B)         -4.36
2226 LEU   ( 883-)  B      2230 - HIS    887- ( B)         -5.19
2556 SER   (   2-)  C      2558 - GLU      4- ( C)         -4.93
2903 PHE   ( 113-)  D      2905 - HIS    115- ( D)         -6.80
3913 LEU   ( 111-)  K      3915 - THR    113- ( K)         -4.45

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

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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.

 471 LEU   ( 472-)  A   -3.08
1167 GLU   (1179-)  A   -2.89
 503 LEU   ( 504-)  A   -2.84
 172 THR   ( 173-)  A   -2.82
3141 THR   ( 131-)  E   -2.81
3561 ASP   (  86-)  H   -2.72
2722 ALA   ( 168-)  C   -2.70
 657 LEU   ( 658-)  A   -2.62
1774 LEU   ( 408-)  B   -2.55
2482 MET   (1152-)  B   -2.53
3612 GLN   ( 137-)  H   -2.52

Warning: Abnormal packing Z-score for sequential residues

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

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

 655 TRP   ( 656-)  A     -  658 HIS   ( 659-)  A        -1.67
1976 ASP   ( 618-)  B     - 1979 GLU   ( 621-)  B        -1.71
2903 PHE   ( 113-)  D     - 2906 SER   ( 116-)  D        -1.59

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

   4 GLN   (   5-)  A
  67 GLN   (  68-)  A
  82 HIS   (  83-)  A
 159 GLN   ( 160-)  A
 170 GLN   ( 171-)  A
 224 ASN   ( 225-)  A
 255 GLN   ( 256-)  A
 338 ASN   ( 339-)  A
 393 ASN   ( 394-)  A
 424 GLN   ( 425-)  A
 438 ASN   ( 439-)  A
 444 ASN   ( 445-)  A
 502 GLN   ( 503-)  A
 583 ASN   ( 584-)  A
 586 HIS   ( 587-)  A
 740 ASN   ( 741-)  A
 744 GLN   ( 745-)  A
 756 ASN   ( 757-)  A
 857 ASN   ( 858-)  A
 902 ASN   ( 903-)  A
 974 HIS   ( 975-)  A
1128 HIS   (1140-)  A
1352 GLN   (1378-)  A
1406 GLN   (1432-)  A
1470 GLN   (  60-)  B
1842 ASN   ( 484-)  B
1873 HIS   ( 515-)  B
1876 HIS   ( 518-)  B
2025 GLN   ( 667-)  B
2164 GLN   ( 821-)  B
2316 GLN   ( 986-)  B
2414 GLN   (1084-)  B
2491 HIS   (1161-)  B
2523 GLN   (1193-)  B
2535 GLN   (1205-)  B
2619 HIS   (  65-)  C
2627 GLN   (  73-)  C
2685 HIS   ( 131-)  C
2969 GLN   ( 179-)  D
3370 GLN   (  57-)  G
3410 HIS   (  97-)  G
3632 ASN   (  12-)  I
3671 ASN   (  51-)  I
3709 GLN   (  89-)  I
3710 GLN   (  90-)  I
3790 HIS   (  53-)  J
3831 ASN   (  29-)  K
3867 HIS   (  65-)  K
3878 GLN   (  76-)  K

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.

   6 SER   (   7-)  A      N
  27 ARG   (  28-)  A      NE
  33 LYS   (  34-)  A      N
  36 PHE   (  37-)  A      N
  38 GLU   (  39-)  A      N
  48 LYS   (  49-)  A      NZ
  49 ILE   (  50-)  A      N
  52 LEU   (  53-)  A      N
  53 ASN   (  54-)  A      N
  53 ASN   (  54-)  A      ND2
  54 ASP   (  55-)  A      N
  56 ARG   (  57-)  A      N
  57 LEU   (  58-)  A      N
  58 GLY   (  59-)  A      N
  60 ILE   (  61-)  A      N
  70 GLN   (  71-)  A      N
  75 GLU   (  76-)  A      N
  79 HIS   (  80-)  A      N
  92 VAL   (  93-)  A      N
  96 ALA   (  97-)  A      N
 113 LEU   ( 114-)  A      N
 114 LEU   ( 115-)  A      N
 115 ASP   ( 116-)  A      N
 116 GLU   ( 117-)  A      N
 117 HIS   ( 118-)  A      N
And so on for a total of 691 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.

  71 GLU   (  72-)  A      OE2
 170 GLN   ( 171-)  A      OE1
 258 GLU   ( 259-)  A      OE1
 298 HIS   ( 299-)  A      ND1
 377 GLU   ( 378-)  A      OE1
 398 HIS   ( 399-)  A      ND1
 434 HIS   ( 435-)  A      NE2
 489 HIS   ( 490-)  A      ND1
 492 GLN   ( 493-)  A      OE1
 514 GLN   ( 515-)  A      OE1
 586 HIS   ( 587-)  A      NE2
 714 GLU   ( 715-)  A      OE2
 766 GLN   ( 767-)  A      OE1
 785 HIS   ( 786-)  A      ND1
 801 ASN   ( 802-)  A      OD1
 837 GLN   ( 838-)  A      OE1
 853 ASN   ( 854-)  A      OD1
 925 GLN   ( 926-)  A      OE1
 931 GLU   ( 932-)  A      OE2
 965 ASN   ( 966-)  A      OD1
1116 GLN   (1128-)  A      OE1
1169 GLN   (1188-)  A      OE1
1238 GLU   (1264-)  A      OE1
1286 ASN   (1312-)  A      OD1
1333 ASP   (1359-)  A      OD2
And so on for a total of 55 lines.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

4013  MG   (2458-)  A     0.43   0.86 Is perhaps NA *2
Since there are no waters, the water check has been skipped.

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.

  41 ASP   (  42-)  A   H-bonding suggests Asn
  42 GLU   (  43-)  A   H-bonding suggests Gln
  54 ASP   (  55-)  A   H-bonding suggests Asn; but Alt-Rotamer
 150 ASP   ( 151-)  A   H-bonding suggests Asn
 155 ASP   ( 156-)  A   H-bonding suggests Asn
 195 GLU   ( 196-)  A   H-bonding suggests Gln
 290 GLU   ( 291-)  A   H-bonding suggests Gln
 397 GLU   ( 398-)  A   H-bonding suggests Gln
 495 GLU   ( 496-)  A   H-bonding suggests Gln; but Alt-Rotamer
 499 GLU   ( 500-)  A   H-bonding suggests Gln; but Alt-Rotamer
 556 ASP   ( 557-)  A   H-bonding suggests Asn
 684 GLU   ( 685-)  A   H-bonding suggests Gln
 691 ASP   ( 692-)  A   H-bonding suggests Asn
 821 GLU   ( 822-)  A   H-bonding suggests Gln
 825 ASP   ( 826-)  A   H-bonding suggests Asn; but Alt-Rotamer
 899 ASP   ( 900-)  A   H-bonding suggests Asn; but Alt-Rotamer
 929 ASP   ( 930-)  A   H-bonding suggests Asn; but Alt-Rotamer
 991 ASP   ( 992-)  A   H-bonding suggests Asn
1012 ASP   (1013-)  A   H-bonding suggests Asn
1042 ASP   (1043-)  A   H-bonding suggests Asn
1049 GLU   (1050-)  A   H-bonding suggests Gln
1143 ASP   (1155-)  A   H-bonding suggests Asn; but Alt-Rotamer
1204 ASP   (1223-)  A   H-bonding suggests Asn; but Alt-Rotamer
1214 ASP   (1233-)  A   H-bonding suggests Asn
1254 GLU   (1280-)  A   H-bonding suggests Gln
And so on for a total of 64 lines.

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 :  -2.187
  2nd generation packing quality :  -2.548
  Ramachandran plot appearance   :  -6.532 (bad)
  chi-1/chi-2 rotamer normality  :  -4.596 (bad)
  Backbone conformation          :  -1.081

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.366 (tight)
  Bond angles                    :   0.705
  Omega angle restraints         :   0.205 (tight)
  Side chain planarity           :   0.232 (tight)
  Improper dihedral distribution :   0.692
  B-factor distribution          :   0.446
  Inside/Outside distribution    :   1.049

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 : 3.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -3.3 (poor)
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.366 (tight)
  Bond angles                    :   0.705
  Omega angle restraints         :   0.205 (tight)
  Side chain planarity           :   0.232 (tight)
  Improper dihedral distribution :   0.692
  B-factor distribution          :   0.446
  Inside/Outside distribution    :   1.049
==============

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.