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.
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: 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 : 3.63
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
187 TYR ( 191-) A
63 PHE ( 66-) A 222 PHE ( 226-) A
31 ASP ( 34-) A 38 ASP ( 41-) A 49 ASP ( 52-) A 72 ASP ( 75-) A 161 ASP ( 165-) A
183 GLU ( 187-) A 217 GLU ( 221-) 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.
189 THR ( 193-) A CA CB 1.61 4.1 206 ILE ( 210-) A CA CB 1.63 5.0
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
| 0.997622 0.000310 -0.000396| | 0.000310 0.997454 -0.000906| | -0.000396 -0.000906 0.997493|Proposed new scale matrix
| 0.024040 -0.000002 0.005520| | -0.000008 0.024369 0.000022| | 0.000006 0.000013 0.014289|With corresponding cell
A = 41.601 B = 41.036 C = 71.813 Alpha= 90.109 Beta= 102.955 Gamma= 89.964
The CRYST1 cell dimensions
A = 41.700 B = 41.140 C = 71.980 Alpha= 90.000 Beta= 102.910 Gamma= 90.000
(Under-)estimated Z-score: 5.575
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.
14 HIS ( 17-) A CG ND1 CE1 109.66 4.1 33 HIS ( 36-) A CG ND1 CE1 109.74 4.1 58 ASN ( 61-) A N CA C 98.66 -4.5
31 ASP ( 34-) A 38 ASP ( 41-) A 49 ASP ( 52-) A 72 ASP ( 75-) A 161 ASP ( 165-) A 183 GLU ( 187-) A 217 GLU ( 221-) A
203 VAL ( 207-) A 5.45 194 LEU ( 198-) A 4.28 58 ASN ( 61-) A 4.04 160 LEU ( 164-) A 4.01
Tau angle RMS Z-score : 1.623
Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
174 ASN ( 178-) A 4.71
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.
172 PHE ( 176-) A -2.8 80 PRO ( 83-) A -2.4 32 THR ( 35-) A -2.4 159 VAL ( 163-) A -2.1 97 LEU ( 100-) 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.
26 SER ( 29-) A PRO omega poor 34 THR ( 37-) A Poor phi/psi 62 ALA ( 65-) A Poor phi/psi 72 ASP ( 75-) A Poor phi/psi 107 ASP ( 110-) A Poor phi/psi 108 LYS ( 111-) A Poor phi/psi 174 ASN ( 178-) A Poor phi/psi 197 PRO ( 201-) A PRO omega poor 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.512
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!
4 TYR ( 7-) A 0 7 HIS ( 10-) A 0 16 ASP ( 19-) A 0 17 PHE ( 20-) A 0 21 LYS ( 24-) A 0 24 ARG ( 27-) A 0 25 GLN ( 28-) A 0 26 SER ( 29-) A 0 47 SER ( 50-) A 0 50 GLN ( 53-) A 0 55 ARG ( 58-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 71 GLN ( 74-) A 0 72 ASP ( 75-) A 0 74 ALA ( 77-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 89 GLN ( 92-) A 0 100 GLN ( 103-) A 0 104 HIS ( 107-) A 0 108 LYS ( 111-) A 0And so on for a total of 112 lines.
Standard deviation of omega values : 2.243
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]
27 PRO ( 30-) A 0.46 HIGH 39 PRO ( 42-) A 0.46 HIGH 151 PRO ( 155-) A 0.45 HIGH 198 PRO ( 202-) A 0.45 HIGH
10 PRO ( 13-) A 106.6 envelop C-beta (108 degrees) 18 PRO ( 21-) A -127.4 half-chair C-delta/C-gamma (-126 degrees) 197 PRO ( 201-) A 105.3 envelop C-beta (108 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.
124 TYR ( 128-) A O <-> 129 LYS ( 133-) A CD 0.52 2.28 INTRA BL 55 ARG ( 58-) A NH1 <-> 169 SER ( 173-) A OG 0.43 2.27 INTRA 153 LEU ( 157-) A CD1 <-> 214 VAL ( 218-) A CG1 0.28 2.92 INTRA BL 55 ARG ( 58-) A NH1 <-> 169 SER ( 173-) A CB 0.26 2.84 INTRA 12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.20 2.80 INTRA BL 1 HIS ( 4-) A CE1 <-> 61 HIS ( 64-) A CE1 0.15 3.05 INTRA 207 VAL ( 211-) A CG2 <-> 258 HOH ( 409 ) A O 0.14 2.66 INTRA 19 ILE ( 22-) A O <-> 22 GLY ( 25-) A N 0.12 2.58 INTRA BL 93 HIS ( 96-) A NE2 <-> 258 HOH ( 301 ) A O 0.11 2.59 INTRA BL 249 ASN ( 253-) A CB <-> 258 HOH ( 375 ) A O 0.08 2.72 INTRA 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.07 2.63 INTRA BL 195 THR ( 199-) A N <-> 196 THR ( 200-) A N 0.06 2.54 INTRA BL 26 SER ( 29-) A N <-> 193 SER ( 197-) A OG 0.06 2.64 INTRA BL 104 HIS ( 107-) A ND1 <-> 114 GLU ( 117-) A OE2 0.04 2.66 INTRA BL 145 LYS ( 149-) A NZ <-> 258 HOH ( 395 ) A O 0.04 2.66 INTRA 121 ASN ( 124-) A N <-> 136 GLY ( 140-) A O 0.04 2.66 INTRA BL 255 SER ( 259-) A N <-> 256 PHE ( 260-) A N 0.04 2.56 INTRA BL 66 GLU ( 69-) A OE1 <-> 89 GLN ( 92-) A NE2 0.03 2.67 INTRA 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.03 2.67 INTRA BL 203 VAL ( 207-) A CG2 <-> 205 TRP ( 209-) A CD1 0.02 3.18 INTRA BL 94 VAL ( 97-) A O <-> 239 ASP ( 243-) A N 0.02 2.68 INTRA BL 37 TYR ( 40-) A CD1 <-> 256 PHE ( 260-) A C 0.02 3.18 INTRA 36 LYS ( 39-) A O <-> 254 ALA ( 258-) A N 0.02 2.68 INTRA BL 55 ARG ( 58-) A CZ <-> 169 SER ( 173-) A CB 0.01 3.19 INTRA 72 ASP ( 75-) A OD1 <-> 86 ARG ( 89-) A NE 0.01 2.69 INTRA BL 93 HIS ( 96-) A N <-> 114 GLU ( 117-) A O 0.01 2.69 INTRA BL
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.
7 HIS ( 10-) A -6.01 33 HIS ( 36-) A -5.29
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.
258 HOH ( 408 ) A O
7 HIS ( 10-) A 33 HIS ( 36-) A 64 ASN ( 67-) A 132 GLN ( 136-) 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.
24 ARG ( 27-) A NE 24 ARG ( 27-) A NH2 28 VAL ( 31-) A N 49 ASP ( 52-) A N 55 ARG ( 58-) A NE 97 LEU ( 100-) A N 110 LYS ( 113-) A N 126 ASP ( 130-) A N 129 LYS ( 133-) A NZ 196 THR ( 200-) A N 200 LEU ( 204-) A N 223 ARG ( 227-) A NH1 225 LEU ( 229-) A N 226 ASN ( 230-) A ND2 256 PHE ( 260-) A N
11 GLU ( 14-) A H-bonding suggests Gln 158 ASP ( 162-) A H-bonding suggests Asn; but Alt-Rotamer
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 : 0.011 2nd generation packing quality : -0.062 Ramachandran plot appearance : -1.898 chi-1/chi-2 rotamer normality : -2.512 Backbone conformation : -0.760
Bond lengths : 0.741 Bond angles : 0.921 Omega angle restraints : 0.408 (tight) Side chain planarity : 0.999 Improper dihedral distribution : 1.304 B-factor distribution : 1.055 Inside/Outside distribution : 0.947
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.
Resolution found in PDB file : 2.00
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.4 2nd generation packing quality : -0.1 Ramachandran plot appearance : -1.2 chi-1/chi-2 rotamer normality : -1.5 Backbone conformation : -0.9
Bond lengths : 0.741 Bond angles : 0.921 Omega angle restraints : 0.408 (tight) Side chain planarity : 0.999 Improper dihedral distribution : 1.304 B-factor distribution : 1.055 Inside/Outside distribution : 0.947 ==============
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.