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.
261 IOE ( 555-) A -
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
Coordinate problems, unexpected atoms, B-factor and occupancy checks
Warning: Occupancies atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.
1 HIS ( 3-) A 0.50 2 HIS ( 4-) A 0.50 12 GLU ( 14-) A 0.50 62 HIS ( 64-) A 0.70 133 GLN ( 136-) A 0.40
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :298.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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
5 TYR ( 7-) A 112 TYR ( 114-) A
32 ASP ( 34-) A 69 ASP ( 71-) A 83 ASP ( 85-) A
184 GLU ( 187-) A 218 GLU ( 221-) A 233 GLU ( 236-) A 235 GLU ( 238-) A
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.
203 CYS ( 206-) A CB SG 1.97 4.8
RMS Z-score for bond lengths: 0.546
RMS-deviation in bond distances: 0.013
Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.
Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.
If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.
Unit Cell deformation matrix
| 0.996996 -0.000543 -0.000077| | -0.000543 0.998599 -0.000071| | -0.000077 -0.000071 0.994899|Proposed new scale matrix
| 0.023269 0.000013 0.006077| | 0.000013 0.023780 0.000002| | 0.000001 0.000001 0.014159|With corresponding cell
A = 42.976 B = 42.052 C = 72.995 Alpha= 89.992 Beta= 104.640 Gamma= 90.062
The CRYST1 cell dimensions
A = 43.105 B = 42.111 C = 73.356 Alpha= 90.000 Beta= 104.600 Gamma= 90.000
(Under-)estimated Z-score: 7.246
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.
15 HIS ( 17-) A CG ND1 CE1 109.65 4.0 61 GLY ( 63-) A N CA C 97.72 -5.1 94 HIS ( 96-) A N CA C 98.36 -4.6 94 HIS ( 96-) A NE2 CD2 CG 111.10 4.6 203 CYS ( 206-) A C CA CB 117.96 4.1 204 VAL ( 207-) A N CA C 122.74 4.1
32 ASP ( 34-) A 69 ASP ( 71-) A 83 ASP ( 85-) A 184 GLU ( 187-) A 218 GLU ( 221-) A 233 GLU ( 236-) A 235 GLU ( 238-) A
204 VAL ( 207-) A 6.36 61 GLY ( 63-) A 5.69 94 HIS ( 96-) A 4.89 76 VAL ( 78-) A 4.59 155 GLN ( 158-) A 4.42
Tau angle RMS Z-score : 1.561
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
81 PRO ( 83-) A -2.7 164 ILE ( 167-) A -2.4 53 THR ( 55-) A -2.3 20 ILE ( 22-) A -2.2 62 HIS ( 64-) A -2.2 173 PHE ( 176-) A -2.1 89 ILE ( 91-) A -2.0 148 GLY ( 151-) A -2.0
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.
27 SER ( 29-) A PRO omega poor 62 HIS ( 64-) A Poor phi/psi 73 ASP ( 75-) A Poor phi/psi 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 198 PRO ( 201-) A PRO omega poor 200 LEU ( 203-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.520
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 TRP ( 5-) A 0 5 TYR ( 7-) A 0 8 HIS ( 10-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 27 SER ( 29-) A 0 48 SER ( 50-) A 0 50 ASP ( 52-) A 0 51 GLN ( 53-) A 0 52 ALA ( 54-) A 0 56 ARG ( 58-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 73 ASP ( 75-) A 0 74 LYS ( 76-) A 0 75 ALA ( 77-) A 0 78 LYS ( 80-) A 0 81 PRO ( 83-) A 0 83 ASP ( 85-) A 0 89 ILE ( 91-) A 0 90 GLN ( 92-) A 0 94 HIS ( 96-) A 0 101 GLN ( 103-) A 0And so on for a total of 114 lines.
Standard deviation of omega values : 1.805
Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
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!
4 GLY ( 6-) A 1.53 14
11 PRO ( 13-) A 0.46 HIGH 198 PRO ( 201-) A 0.46 HIGH
178 PRO ( 181-) A 46.7 half-chair C-delta/C-gamma (54 degrees) 199 PRO ( 202-) A 48.1 half-chair C-delta/C-gamma (54 degrees)
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.
94 HIS ( 96-) A NE2 <-> 117 HIS ( 119-) A ND1 0.39 2.61 INTRA BL 94 HIS ( 96-) A NE2 <-> 117 HIS ( 119-) A CE1 0.34 2.76 INTRA BL 72 GLN ( 74-) A NE2 <-> 74 LYS ( 76-) A NZ 0.31 2.54 INTRA 60 ASN ( 62-) A ND2 <-> 61 GLY ( 63-) A O 0.31 2.29 INTRA 60 ASN ( 62-) A ND2 <-> 63 ALA ( 65-) A O 0.23 2.47 INTRA BL 94 HIS ( 96-) A NE2 <-> 261 IOE ( 555-) A NP2 0.22 2.78 INTRA 94 HIS ( 96-) A CD2 <-> 117 HIS ( 119-) A CE1 0.20 3.00 INTRA BL 134 GLN ( 137-) A C <-> 260 HG ( 263-) A HG 0.18 3.02 INTRA 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.14 2.86 INTRA BL 144 PHE ( 147-) A CD2 <-> 262 HOH ( 275 ) A O 0.07 2.73 INTRA 60 ASN ( 62-) A C <-> 61 GLY ( 63-) A O 0.07 2.53 INTRA 72 GLN ( 74-) A O <-> 74 LYS ( 76-) A N 0.07 2.63 INTRA 70 ASP ( 72-) A O <-> 87 ARG ( 89-) A NH1 0.05 2.65 INTRA 164 ILE ( 167-) A CD1 <-> 262 HOH ( 264 ) A O 0.04 2.76 INTRA 28 PRO ( 30-) A O <-> 246 GLN ( 249-) A N 0.03 2.67 INTRA BL 94 HIS ( 96-) A CE1 <-> 261 IOE ( 555-) A NP2 0.03 3.07 INTRA 117 HIS ( 119-) A ND1 <-> 261 IOE ( 555-) A NP2 0.03 2.97 INTRA 58 LEU ( 60-) A C <-> 262 HOH ( 264 ) A O 0.03 2.77 INTRA 148 GLY ( 151-) A N <-> 215 VAL ( 218-) A O 0.02 2.68 INTRA 38 TYR ( 40-) A CD1 <-> 257 PHE ( 260-) A C 0.02 3.18 INTRA 57 ILE ( 59-) A CG2 <-> 262 HOH ( 269 ) A O 0.02 2.78 INTRA
Chain identifier: A
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.
8 HIS ( 10-) A -6.06 2 HIS ( 4-) A -5.78 98 LEU ( 100-) A -5.02
Chain identifier: A
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
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.
262 HOH ( 264 ) A O 262 HOH ( 265 ) A O 262 HOH ( 279 ) A O Marked this atom as acceptor 261 IOE ( 555-) A F23 Marked this atom as acceptor 261 IOE ( 555-) A F22 Marked this atom as acceptor 261 IOE ( 555-) A F21 Metal-coordinating Histidine residue 92 fixed to 1 Metal-coordinating Histidine residue 94 fixed to 1 Metal-coordinating Histidine residue 117 fixed to 1
15 HIS ( 17-) A 60 ASN ( 62-) A 72 GLN ( 74-) A 101 GLN ( 103-) A 175 ASN ( 178-) A
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.
29 VAL ( 31-) A N 50 ASP ( 52-) A N 51 GLN ( 53-) A N 64 PHE ( 66-) A N 72 GLN ( 74-) A N 93 PHE ( 95-) A N 98 LEU ( 100-) A N 122 ASN ( 124-) A ND2 127 ASP ( 130-) A N 197 THR ( 200-) A N 201 LEU ( 204-) A N 230 GLY ( 233-) A N 242 TRP ( 245-) A N 257 PHE ( 260-) A N Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.695 2nd generation packing quality : 0.037 Ramachandran plot appearance : -1.877 chi-1/chi-2 rotamer normality : -2.520 Backbone conformation : -0.592
Bond lengths : 0.546 (tight) Bond angles : 0.787 Omega angle restraints : 0.328 (tight) Side chain planarity : 0.578 (tight) Improper dihedral distribution : 0.995 B-factor distribution : 0.531 Inside/Outside distribution : 0.961
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 : 1.92
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.2 2nd generation packing quality : -0.3 Ramachandran plot appearance : -1.7 chi-1/chi-2 rotamer normality : -1.7 Backbone conformation : -1.0
Bond lengths : 0.546 (tight) Bond angles : 0.787 Omega angle restraints : 0.328 (tight) Side chain planarity : 0.578 (tight) Improper dihedral distribution : 0.995 B-factor distribution : 0.531 Inside/Outside distribution : 0.961 ==============
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.