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 two or less which PRODRUG also cannot cope with), 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.
147 B21 (1165-) A - 148 12P (1164-) A - OK
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. The header of the PDB file states that TLS groups
were used. So, if WHAT IF complains about your B-factors, while 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:
Number of TLS groups mentione in PDB file header: 0
Crystal temperature (K) :277.000
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
17 TYR ( 23-) A 74 TYR ( 92-) A
85 PHE ( 103-) A 92 PHE ( 110-) A 107 PHE ( 125-) A 116 PHE ( 134-) A
84 ASP ( 102-) A
6 GLU ( 12-) A 33 GLU ( 51-) A 58 GLU ( 76-) A 66 GLU ( 84-) A 83 GLU ( 101-) A
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
| 0.994233 0.000204 0.000899| | 0.000204 0.995216 0.001089| | 0.000899 0.001089 0.993767|Proposed new scale matrix
| 0.014746 0.008504 -0.000023| | -0.000003 0.017012 -0.000019| | -0.000011 -0.000014 0.012567|With corresponding cell
A = 67.806 B = 67.846 C = 79.571 Alpha= 89.943 Beta= 89.896 Gamma= 119.959
The CRYST1 cell dimensions
A = 68.200 B = 68.200 C = 80.068 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 9.211
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.
11 ARG ( 17-) A CB CG CD 105.85 -4.1 41 HIS ( 59-) A CG ND1 CE1 109.92 4.3 139 HIS ( 157-) A CG ND1 CE1 109.91 4.3
6 GLU ( 12-) A 33 GLU ( 51-) A 58 GLU ( 76-) A 66 GLU ( 84-) A 83 GLU ( 101-) A 84 ASP ( 102-) A
114 LYS ( 132-) A 4.60
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.
41 HIS ( 59-) A -2.2
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.
13 SER ( 19-) A omega poor 24 ASN ( 30-) A Poor phi/psi 39 CYS ( 57-) A omega poor 52 PRO ( 70-) A Poor phi/psi 91 GLN ( 109-) A omega poor 96 SER ( 114-) A omega poor 101 ARG ( 119-) A Poor phi/psi 110 GLY ( 128-) A omega poor 112 MET ( 130-) A omega poor 129 SER ( 147-) A omega poor 139 HIS ( 157-) A omega poor chi-1/chi-2 correlation Z-score : -2.182
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 PRO ( 9-) A 0 5 TRP ( 11-) A 0 11 ARG ( 17-) A 0 13 SER ( 19-) A 0 21 HIS ( 27-) A 0 24 ASN ( 30-) A 0 26 SER ( 32-) A 0 27 GLN ( 33-) A 0 31 PRO ( 37-) A 0 32 SER ( 38-) A 0 33 GLU ( 51-) A 0 34 PRO ( 52-) A 0 35 ALA ( 53-) A 0 36 ARG ( 54-) A 0 46 HIS ( 64-) A 0 50 ARG ( 68-) A 0 51 ARG ( 69-) A 0 52 PRO ( 70-) A 0 53 SER ( 71-) A 0 56 ARG ( 74-) A 0 57 GLN ( 75-) A 0 61 THR ( 79-) A 0 80 SER ( 98-) A 0 83 GLU ( 101-) A 0 101 ARG ( 119-) A 0And so on for a total of 67 lines.
Standard deviation of omega values : 7.617
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]
52 PRO ( 70-) A 0.14 LOW
2 PRO ( 8-) A -112.1 envelop C-gamma (-108 degrees) 31 PRO ( 37-) A -130.0 half-chair C-delta/C-gamma (-126 degrees) 34 PRO ( 52-) A -3.3 envelop N (0 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.
32 SER ( 38-) A CA <-> 149 HOH (2020 ) A O 0.68 2.12 INTRA BF 148 12P (1164-) A C36 <-> 149 HOH (2056 ) A O 0.46 2.24 INTRA BL 113 GLN ( 131-) A OE1 <-> 149 HOH (2080 ) A O 0.46 1.94 INTRA BF 79 LYS ( 97-) A NZ <-> 148 12P (1164-) A C35 0.41 2.69 INTRA BL 112 MET ( 130-) A N <-> 149 HOH (2078 ) A O 0.25 2.45 INTRA BF 50 ARG ( 68-) A NH1 <-> 149 HOH (2029 ) A O 0.20 2.50 INTRA BF 32 SER ( 38-) A N <-> 149 HOH (2020 ) A O 0.18 2.52 INTRA BF 27 GLN ( 33-) A NE2 <-> 29 GLU ( 35-) A O 0.17 2.53 INTRA BF 50 ARG ( 68-) A NH2 <-> 147 B21 (1165-) A OAN 0.17 2.53 INTRA BF 41 HIS ( 59-) A ND1 <-> 139 HIS ( 157-) A ND1 0.12 2.88 INTRA BL 21 HIS ( 27-) A NE2 <-> 149 HOH (2003 ) A O 0.10 2.60 INTRA 114 LYS ( 132-) A N <-> 115 PRO ( 133-) A CD 0.10 2.90 INTRA 118 ASP ( 136-) A OD1 <-> 149 HOH (2083 ) A O 0.09 2.31 INTRA 79 LYS ( 97-) A NZ <-> 148 12P (1164-) A C32 0.09 3.01 INTRA BL 77 LYS ( 95-) A CE <-> 149 HOH (2059 ) A O 0.08 2.72 INTRA BF 91 GLN ( 109-) A NE2 <-> 149 HOH (2063 ) A O 0.07 2.63 INTRA 45 LYS ( 63-) A NZ <-> 147 B21 (1165-) A OAO 0.07 2.63 INTRA BF 48 GLN ( 66-) A OE1 <-> 149 HOH (2027 ) A O 0.05 2.35 INTRA BF 64 LYS ( 82-) A NZ <-> 149 HOH (2044 ) A O 0.05 2.65 INTRA BF 104 LEU ( 122-) A CD1 <-> 147 B21 (1165-) A CAL 0.04 3.16 INTRA BF 10 SER ( 16-) A CB <-> 15 ARG ( 21-) A O 0.04 2.76 INTRA BF 72 ASN ( 90-) A ND2 <-> 149 HOH (2048 ) A O 0.03 2.67 INTRA 33 GLU ( 51-) A OE2 <-> 109 ARG ( 127-) A NE 0.02 2.68 INTRA BF 52 PRO ( 70-) A O <-> 60 ILE ( 78-) A N 0.02 2.68 INTRA 88 LEU ( 106-) A O <-> 92 PHE ( 110-) A N 0.02 2.68 INTRA BL 82 GLU ( 100-) A OE1 <-> 149 HOH (2058 ) A O 0.02 2.38 INTRA BF 20 ASN ( 26-) A N <-> 25 ALA ( 31-) A O 0.01 2.69 INTRA BL 6 GLU ( 12-) A OE2 <-> 149 HOH (2003 ) A O 0.01 2.39 INTRA BF
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.
11 ARG ( 17-) A -6.92 50 ARG ( 68-) A -6.77 56 ARG ( 74-) A -5.91 51 ARG ( 69-) A -5.63 109 ARG ( 127-) A -5.40 124 ARG ( 142-) A -5.26 91 GLN ( 109-) A -5.22 30 ARG ( 36-) A -5.01
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.
149 HOH (2076 ) A O 36.25 -26.72 21.21
149 HOH (2005 ) A O 149 HOH (2024 ) A O 149 HOH (2032 ) A O 149 HOH (2079 ) A O
24 ASN ( 30-) A 91 GLN ( 109-) 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.
15 ARG ( 21-) A N 111 GLN ( 129-) A N 124 ARG ( 142-) A NE 136 SER ( 154-) A OG
83 GLU ( 101-) A H-bonding suggests Gln
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 : -1.062 2nd generation packing quality : 0.122 Ramachandran plot appearance : -0.619 chi-1/chi-2 rotamer normality : -2.182 Backbone conformation : -0.330
Bond lengths : 0.990 Bond angles : 0.958 Omega angle restraints : 1.385 (loose) Side chain planarity : 0.972 Improper dihedral distribution : 1.121 B-factor distribution : 0.599 Inside/Outside distribution : 0.992
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 : -0.8 2nd generation packing quality : 0.0 Ramachandran plot appearance : -0.0 chi-1/chi-2 rotamer normality : -1.2 Backbone conformation : -0.5
Bond lengths : 0.990 Bond angles : 0.958 Omega angle restraints : 1.385 (loose) Side chain planarity : 0.972 Improper dihedral distribution : 1.121 B-factor distribution : 0.599 Inside/Outside distribution : 0.992 ==============
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.