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.
The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.
256 BME ( 262-) A - Fragmented
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:
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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.
9 PRO ( 13-) A C O 1.31 4.1 51 THR ( 55-) A CB OG1 1.51 4.5 107 LYS ( 111-) A C O 1.33 4.7 157 ASP ( 162-) A C O 1.32 4.7 164 THR ( 169-) A CA CB 1.63 4.8 191 GLY ( 196-) A N -C 1.24 -4.5 216 GLU ( 221-) A N CA 1.56 5.4
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
| 0.997164 0.000132 0.001404| | 0.000132 0.993382 -0.001614| | 0.001404 -0.001614 0.998275|Proposed new scale matrix
| 0.023477 0.000007 0.006078| | -0.000003 0.024141 0.000039| | -0.000020 0.000023 0.014181|With corresponding cell
A = 42.579 B = 41.424 C = 72.818 Alpha= 90.184 Beta= 104.433 Gamma= 89.985
The CRYST1 cell dimensions
A = 42.700 B = 41.700 C = 73.000 Alpha= 90.000 Beta= 104.600 Gamma= 90.000
(Under-)estimated Z-score: 9.054
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.
8 GLY ( 12-) A -C N CA 128.28 4.5 10 GLU ( 14-) A CA CB CG 126.66 6.3 10 GLU ( 14-) A CB CG CD 121.03 5.0 11 HIS ( 15-) A CG ND1 CE1 111.88 6.3 11 HIS ( 15-) A ND1 CE1 NE2 105.67 -4.6 15 ASP ( 19-) A CA CB CG 108.07 -4.5 20 LYS ( 24-) A CA CB CG 123.03 4.5 22 GLU ( 26-) A CA C O 112.38 -5.0 23 ARG ( 27-) A CA CB CG 124.81 5.4 23 ARG ( 27-) A CG CD NE 121.10 6.2 29 ILE ( 33-) A N CA CB 118.43 4.7 29 ILE ( 33-) A CA CB CG2 117.31 4.0 32 HIS ( 36-) A CA CB CG 106.87 -6.9 33 THR ( 37-) A CA CB CG2 118.15 4.5 33 THR ( 37-) A CA CB OG1 100.85 -5.8 37 ASP ( 41-) A CA CB CG 108.08 -4.5 47 TYR ( 51-) A CA C O 113.46 -4.3 47 TYR ( 51-) A CA CB CG 123.81 5.4 49 GLN ( 53-) A CB CG CD 103.04 -5.6 49 GLN ( 53-) A CG CD NE2 108.25 -5.4 49 GLN ( 53-) A NE2 CD OE1 131.33 8.7 54 ARG ( 58-) A -O -C N 130.34 4.6 54 ARG ( 58-) A -CA -C N 107.42 -4.4 54 ARG ( 58-) A N CA CB 103.47 -4.1 57 ASN ( 61-) A C CA CB 118.04 4.2And so on for a total of 101 lines.
202 VAL ( 207-) A 5.50 54 ARG ( 58-) A 4.72 64 VAL ( 68-) A 4.30
Tau angle RMS Z-score : 1.684
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.
11 HIS ( 15-) A 4.25
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.
54 ARG ( 58-) A -2.8 79 PRO ( 83-) A -2.5 76 LYS ( 80-) A -2.3 88 GLN ( 92-) A -2.3 75 LEU ( 79-) A -2.1 158 VAL ( 163-) A -2.1 190 PRO ( 195-) A -2.1 51 THR ( 55-) A -2.0 33 THR ( 37-) 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.
25 SER ( 29-) A PRO omega poor 61 ALA ( 65-) A Poor phi/psi 106 ASP ( 110-) A Poor phi/psi 107 LYS ( 111-) A Poor phi/psi 124 GLY ( 129-) A Poor phi/psi 173 ASN ( 178-) A Poor phi/psi 196 PRO ( 201-) A PRO omega poor 248 ASN ( 253-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.347
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 TYR ( 7-) A 0 6 HIS ( 10-) A 0 15 ASP ( 19-) A 0 16 PHE ( 20-) A 0 20 LYS ( 24-) A 0 22 GLU ( 26-) A 0 23 ARG ( 27-) A 0 24 GLN ( 28-) A 0 25 SER ( 29-) A 0 46 SER ( 50-) A 0 48 ASP ( 52-) A 0 50 ALA ( 54-) A 0 54 ARG ( 58-) A 0 55 ILE ( 59-) A 0 58 ASN ( 62-) A 0 60 HIS ( 64-) A 0 68 ASP ( 72-) A 0 69 SER ( 73-) A 0 71 ASP ( 75-) A 0 72 LYS ( 76-) A 0 73 ALA ( 77-) A 0 76 LYS ( 80-) A 0 79 PRO ( 83-) A 0 81 ASP ( 85-) A 0 87 ILE ( 91-) A 0And so on for a total of 115 lines.
Standard deviation of omega values : 1.685
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]
17 PRO ( 21-) A 0.17 LOW 26 PRO ( 30-) A 0.47 HIGH 133 PRO ( 138-) A 0.17 LOW 150 PRO ( 155-) A 0.04 LOW
190 PRO ( 195-) A -58.0 half-chair C-beta/C-alpha (-54 degrees) 210 PRO ( 215-) A 49.4 half-chair C-delta/C-gamma (54 degrees) 245 PRO ( 250-) A 50.1 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.
60 HIS ( 64-) A ND1 <-> 257 HOH ( 326 ) A O 0.54 2.16 INTRA BL 64 VAL ( 68-) A C <-> 257 HOH ( 353 ) A O 0.49 2.31 INTRA 248 ASN ( 253-) A ND2 <-> 249 ARG ( 254-) A N 0.43 2.32 INTRA BL 1 TRP ( 5-) A N <-> 257 HOH ( 392 ) A O 0.42 2.28 INTRA 108 LYS ( 112-) A NZ <-> 257 HOH ( 329 ) A O 0.40 2.30 INTRA 71 ASP ( 75-) A OD1 <-> 85 ARG ( 89-) A NE 0.37 2.33 INTRA BL 175 ASP ( 180-) A OD2 <-> 177 ARG ( 182-) A NH2 0.35 2.35 INTRA BL 122 LYS ( 127-) A NZ <-> 257 HOH ( 307 ) A O 0.32 2.38 INTRA 115 HIS ( 119-) A ND1 <-> 257 HOH ( 263 ) A O 0.30 2.40 INTRA BL 47 TYR ( 51-) A OH <-> 118 HIS ( 122-) A NE2 0.29 2.41 INTRA BL 54 ARG ( 58-) A CD <-> 65 GLU ( 69-) A OE1 0.28 2.52 INTRA BL 82 GLY ( 86-) A O <-> 257 HOH ( 365 ) A O 0.27 2.13 INTRA 68 ASP ( 72-) A OD2 <-> 119 TRP ( 123-) A NE1 0.27 2.43 INTRA BL 188 THR ( 193-) A CG2 <-> 257 HOH ( 320 ) A O 0.25 2.55 INTRA 194 THR ( 199-) A N <-> 257 HOH ( 349 ) A O 0.24 2.46 INTRA 65 GLU ( 69-) A CG <-> 257 HOH ( 353 ) A O 0.23 2.57 INTRA 58 ASN ( 62-) A O <-> 165 LYS ( 170-) A NZ 0.21 2.49 INTRA 32 HIS ( 36-) A CD2 <-> 257 HOH ( 338 ) A O 0.20 2.60 INTRA 54 ARG ( 58-) A O <-> 65 GLU ( 69-) A N 0.20 2.50 INTRA BL 225 ASN ( 230-) A ND2 <-> 233 GLU ( 238-) A OE2 0.20 2.50 INTRA 247 LYS ( 252-) A NZ <-> 257 HOH ( 377 ) A O 0.20 2.50 INTRA BL 11 HIS ( 15-) A ND1 <-> 14 LYS ( 18-) A NZ 0.19 2.81 INTRA BL 15 ASP ( 19-) A OD1 <-> 257 HOH ( 272 ) A O 0.18 2.22 INTRA 242 PRO ( 247-) A O <-> 244 GLN ( 249-) A NE2 0.17 2.53 INTRA BL 36 TYR ( 40-) A CD1 <-> 255 PHE ( 260-) A C 0.17 3.03 INTRAAnd so on for a total of 67 lines.
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.
6 HIS ( 10-) A -5.89 131 GLN ( 136-) A -5.10
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 clusters without contacts with non-water atoms
The water molecules listed in the table below are part of water molecule
clusters that do not make contacts with non-waters. These water molecules are
part of clusters that have a distance at least 1 Angstrom larger than the
sum of the Van der Waals radii to the nearest non-solvent atom. Because
these kinds of water clusters usually are not observed with X-ray diffraction
their presence could indicate a refinement artifact. The number in brackets
is the identifier of the water molecule in the input file.
257 HOH ( 352 ) A O
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.
257 HOH ( 286 ) A O -21.28 -10.42 4.17 257 HOH ( 288 ) A O -18.44 -20.27 8.34 257 HOH ( 325 ) A O -20.75 -7.01 -1.98
257 HOH ( 265 ) A O 257 HOH ( 266 ) A O 257 HOH ( 277 ) A O 257 HOH ( 320 ) A O 257 HOH ( 330 ) A O 257 HOH ( 347 ) A O 257 HOH ( 352 ) A O 257 HOH ( 363 ) A O 257 HOH ( 375 ) A O
49 GLN ( 53-) A 173 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.
27 VAL ( 31-) A N 41 LYS ( 45-) A N 49 GLN ( 53-) A N 54 ARG ( 58-) A NH1 62 PHE ( 66-) A N 63 ASN ( 67-) A ND2 70 GLN ( 74-) A N 91 PHE ( 95-) A N 96 LEU ( 100-) A N 195 THR ( 200-) A N 199 LEU ( 204-) A N 216 GLU ( 221-) A N 227 ASN ( 232-) A N 239 ASN ( 244-) A ND2 240 TRP ( 245-) A N
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.
65 GLU ( 69-) A OE1
28 ASP ( 32-) 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 : -0.184 2nd generation packing quality : -0.226 Ramachandran plot appearance : -2.428 chi-1/chi-2 rotamer normality : -2.347 Backbone conformation : -1.113
Bond lengths : 1.314 Bond angles : 1.844 Omega angle restraints : 0.306 (tight) Side chain planarity : 1.245 Improper dihedral distribution : 1.347 B-factor distribution : 0.359 Inside/Outside distribution : 0.949
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 : 2.35
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.9 2nd generation packing quality : 0.8 Ramachandran plot appearance : -0.7 chi-1/chi-2 rotamer normality : -1.4 Backbone conformation : -1.0
Bond lengths : 1.314 Bond angles : 1.844 Omega angle restraints : 0.306 (tight) Side chain planarity : 1.245 Improper dihedral distribution : 1.347 B-factor distribution : 0.359 Inside/Outside distribution : 0.949 ==============
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.