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 IOA ( 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
112 TYR ( 114-) A
64 PHE ( 66-) A
69 ASP ( 71-) A 83 ASP ( 85-) A
12 GLU ( 14-) A 184 GLU ( 187-) A 233 GLU ( 236-) A 236 GLU ( 239-) A
RMS Z-score for bond lengths: 0.525
RMS-deviation in bond distances: 0.012
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
| 0.995367 -0.000508 0.000949| | -0.000508 0.998007 -0.000197| | 0.000949 -0.000197 0.995454|Proposed new scale matrix
| 0.023287 0.000013 0.006145| | 0.000012 0.024032 0.000005| | -0.000013 0.000003 0.014168|With corresponding cell
A = 42.932 B = 41.611 C = 72.977 Alpha= 90.007 Beta= 104.727 Gamma= 90.058
The CRYST1 cell dimensions
A = 43.132 B = 41.694 C = 73.347 Alpha= 90.000 Beta= 104.830 Gamma= 90.000
(Under-)estimated Z-score: 8.400
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.
61 GLY ( 63-) A N CA C 98.40 -4.9 94 HIS ( 96-) A N CA C 98.41 -4.6 94 HIS ( 96-) A NE2 CD2 CG 110.58 4.1
12 GLU ( 14-) A 69 ASP ( 71-) A 83 ASP ( 85-) A 184 GLU ( 187-) A 233 GLU ( 236-) A 236 GLU ( 239-) A
204 VAL ( 207-) A 5.74 61 GLY ( 63-) A 5.44 94 HIS ( 96-) A 4.86
Tau angle RMS Z-score : 1.590
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.
62 HIS ( 64-) A -3.0 81 PRO ( 83-) A -2.5 58 LEU ( 60-) A -2.3 160 VAL ( 163-) A -2.1 148 GLY ( 151-) A -2.1
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 100 GLY ( 102-) A Poor phi/psi 108 ASP ( 110-) 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 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.634
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 18 PHE ( 20-) 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 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 63 ALA ( 65-) 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 82 LEU ( 84-) A 0 83 ASP ( 85-) A 0 90 GLN ( 92-) A 0 94 HIS ( 96-) A 0And so on for a total of 119 lines.
Standard deviation of omega values : 1.747
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].
11 PRO ( 13-) A -136.9 envelop C-delta (-144 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 0.38 2.62 INTRA BL 94 HIS ( 96-) A NE2 <-> 117 HIS ( 119-) A CE1 0.22 2.88 INTRA BL 195 LEU ( 198-) A CD1 <-> 261 IOA ( 555-) A F22 0.22 2.98 INTRA 94 HIS ( 96-) A CD2 <-> 117 HIS ( 119-) A CE1 0.18 3.02 INTRA BL 94 HIS ( 96-) A NE2 <-> 261 IOA ( 555-) A NP2 0.18 2.82 INTRA 201 LEU ( 204-) A CD1 <-> 261 IOA ( 555-) A F22 0.18 3.02 INTRA 28 PRO ( 30-) A O <-> 246 GLN ( 249-) A N 0.13 2.57 INTRA BL 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.12 2.88 INTRA BL 202 GLU ( 205-) A C <-> 203 CYS ( 206-) A SG 0.11 3.19 INTRA BL 94 HIS ( 96-) A CD2 <-> 117 HIS ( 119-) A ND1 0.11 2.99 INTRA BL 117 HIS ( 119-) A ND1 <-> 261 IOA ( 555-) A NP2 0.08 2.92 INTRA 14 TRP ( 16-) A CH2 <-> 262 HOH ( 288 ) A O 0.08 2.72 INTRA 61 GLY ( 63-) A C <-> 62 HIS ( 64-) A CG 0.06 3.04 INTRA BL 34 HIS ( 36-) A CD2 <-> 262 HOH ( 350 ) A O 0.05 2.75 INTRA 31 ILE ( 33-) A O <-> 108 ASP ( 110-) A N 0.05 2.65 INTRA BL 10 GLY ( 12-) A CA <-> 11 PRO ( 13-) A CD 0.04 2.76 INTRA BL 70 ASP ( 72-) A OD2 <-> 121 TRP ( 123-) A NE1 0.04 2.66 INTRA BL 223 PHE ( 226-) A CE1 <-> 262 HOH ( 287 ) A O 0.04 2.76 INTRA 244 PRO ( 247-) A O <-> 246 GLN ( 249-) A NE2 0.03 2.67 INTRA BL 74 LYS ( 76-) A N <-> 262 HOH ( 324 ) A O 0.03 2.67 INTRA 193 GLY ( 196-) A N <-> 204 VAL ( 207-) A O 0.03 2.67 INTRA BL 61 GLY ( 63-) A O <-> 62 HIS ( 64-) A CB 0.03 2.57 INTRA 73 ASP ( 75-) A OD1 <-> 87 ARG ( 89-) A NE 0.03 2.67 INTRA 60 ASN ( 62-) A C <-> 61 GLY ( 63-) A O 0.01 2.59 INTRA 11 PRO ( 13-) A CB <-> 262 HOH ( 288 ) A O 0.01 2.79 INTRA 23 GLY ( 25-) A O <-> 249 LYS ( 252-) A NZ 0.01 2.69 INTRA 31 ILE ( 33-) A N <-> 106 THR ( 108-) A O 0.01 2.69 INTRA BL 5 TYR ( 7-) A N <-> 6 GLY ( 8-) A N 0.01 2.59 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.
8 HIS ( 10-) A -5.89 2 HIS ( 4-) A -5.84 98 LEU ( 100-) A -5.18
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
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
262 HOH ( 277 ) A O -19.22 -20.07 20.39 262 HOH ( 357 ) A O -18.86 -22.69 18.30
262 HOH ( 269 ) A O 262 HOH ( 272 ) A O 262 HOH ( 356 ) A O 262 HOH ( 361 ) A O Marked this atom as acceptor 261 IOA ( 555-) A F21 Marked this atom as acceptor 261 IOA ( 555-) A F22 Metal-coordinating Histidine residue 92 fixed to 1 Metal-coordinating Histidine residue 94 fixed to 1 Metal-coordinating Histidine residue 117 fixed to 1
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 30 ASP ( 32-) A N 72 GLN ( 74-) A N 98 LEU ( 100-) A N 122 ASN ( 124-) A ND2 127 ASP ( 130-) A N 162 ASP ( 165-) A N 170 SER ( 173-) A N 197 THR ( 200-) A N 201 LEU ( 204-) A N 218 GLU ( 221-) 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
108 ASP ( 110-) A H-bonding suggests Asn; but Alt-Rotamer 159 ASP ( 162-) A H-bonding suggests Asn
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 : -0.413 2nd generation packing quality : 0.198 Ramachandran plot appearance : -1.840 chi-1/chi-2 rotamer normality : -1.634 Backbone conformation : -0.719
Bond lengths : 0.525 (tight) Bond angles : 0.776 Omega angle restraints : 0.318 (tight) Side chain planarity : 0.515 (tight) Improper dihedral distribution : 0.983 B-factor distribution : 0.689 Inside/Outside distribution : 0.954
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 : 1.86
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : -0.2 Ramachandran plot appearance : -1.8 chi-1/chi-2 rotamer normality : -1.0 Backbone conformation : -1.0
Bond lengths : 0.525 (tight) Bond angles : 0.776 Omega angle restraints : 0.318 (tight) Side chain planarity : 0.515 (tight) Improper dihedral distribution : 0.983 B-factor distribution : 0.689 Inside/Outside distribution : 0.954 ==============
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.