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 Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.
Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).
Molecular weight of all polymer chains: 24942.395
Volume of the Unit Cell V= 2180364.3
Space group multiplicity: 16
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.463
Vm by authors and this calculated Vm do not agree very well
Non-validating, descriptive output paragraph
Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many plus-
signs fall outside the contoured areas then the molecule is poorly refined
(or worse). Proline can only occur in the narrow region around phi=-60 that
also falls within the other contour islands.
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: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
223 LYS ( 223-) A CG 223 LYS ( 223-) A CD 223 LYS ( 223-) A CE 223 LYS ( 223-) A NZ
1 MET ( 1-) A High 2 VAL ( 2-) A High 3 GLU ( 3-) A High 4 LYS ( 4-) A High 5 GLY ( 5-) A High 6 LYS ( 6-) A High 7 MET ( 7-) A High 8 VAL ( 8-) A High 9 LYS ( 9-) A High 10 ILE ( 10-) A High 11 SER ( 11-) A High 12 TYR ( 12-) A High 13 ASP ( 13-) A High 14 GLY ( 14-) A High 15 TYR ( 15-) A High 16 VAL ( 16-) A High 17 ASP ( 17-) A High 18 GLY ( 18-) A High 19 LYS ( 19-) A High 20 LEU ( 20-) A High 21 PHE ( 21-) A High 22 ASP ( 22-) A High 23 THR ( 23-) A High 24 THR ( 24-) A High 25 ASN ( 25-) A HighAnd so on for a total of 215 lines.
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 3
Crystal temperature (K) :100.000
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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
125 ARG ( 125-) A
12 TYR ( 12-) A 15 TYR ( 15-) A 35 TYR ( 35-) A 141 TYR ( 141-) A
21 PHE ( 21-) A 47 PHE ( 47-) A 80 PHE ( 80-) A 96 PHE ( 96-) A 130 PHE ( 130-) A 186 PHE ( 186-) A 189 PHE ( 189-) A 216 PHE ( 216-) A 220 PHE ( 220-) A
65 ASP ( 65-) A 151 ASP ( 151-) A
95 GLU ( 95-) A 133 GLU ( 133-) A 185 GLU ( 185-) A 203 GLU ( 203-) A 209 GLU ( 209-) A 212 GLU ( 212-) 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.
95 GLU ( 95-) A C O 1.32 4.2
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
| 0.997075 0.000056 -0.000676| | 0.000056 0.997416 0.000469| | -0.000676 0.000469 0.997119|Proposed new scale matrix
| 0.007270 0.000000 0.000005| | 0.000000 0.007268 -0.000003| | 0.000006 -0.000004 0.008753|With corresponding cell
A = 137.547 B = 137.594 C = 114.244 Alpha= 89.946 Beta= 90.078 Gamma= 90.002
The CRYST1 cell dimensions
A = 137.950 B = 137.950 C = 114.570 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 5.517
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
65 ASP ( 65-) A 95 GLU ( 95-) A 125 ARG ( 125-) A 133 GLU ( 133-) A 151 ASP ( 151-) A 185 GLU ( 185-) A 203 GLU ( 203-) A 209 GLU ( 209-) A 212 GLU ( 212-) A
Ramachandran Z-score : -3.940
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.
173 THR ( 173-) A -3.1 23 THR ( 23-) A -2.9 10 ILE ( 10-) A -2.4 46 ILE ( 46-) A -2.4 109 ILE ( 109-) A -2.4 170 VAL ( 170-) A -2.3 195 THR ( 195-) 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.
79 ALA ( 79-) A Poor phi/psi 112 ASP ( 112-) A Poor phi/psi 123 SER ( 123-) A Poor phi/psi 152 LYS ( 152-) A Poor phi/psi 176 ASN ( 176-) A Poor phi/psi 192 ASN ( 192-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -4.999
chi-1/chi-2 correlation Z-score : -4.999
Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring residues on either side is in a conformation that is not
seen very often in the database of solved protein structures. The number
given in the table is the number of similar backbone conformations in the
database with the same amino acid in the centre.
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 LYS ( 4-) A 0 16 VAL ( 16-) A 0 22 ASP ( 22-) A 0 32 GLU ( 32-) A 0 38 ALA ( 38-) A 0 39 MET ( 39-) A 0 41 TYR ( 41-) A 0 43 PRO ( 43-) A 0 48 ALA ( 48-) A 0 50 GLU ( 50-) A 0 52 GLN ( 52-) A 0 53 VAL ( 53-) A 0 54 LEU ( 54-) A 0 64 MET ( 64-) A 0 66 VAL ( 66-) A 0 68 GLU ( 68-) A 0 79 ALA ( 79-) A 0 80 PHE ( 80-) A 0 83 ARG ( 83-) A 0 88 ILE ( 88-) A 0 102 LYS ( 102-) A 0 105 LYS ( 105-) A 0 112 ASP ( 112-) A 0 122 ASN ( 122-) A 0 123 SER ( 123-) A 0And so on for a total of 75 lines.
76 PRO ( 76-) A -116.4 envelop C-gamma (-108 degrees) 184 PRO ( 184-) A -125.5 half-chair C-delta/C-gamma (-126 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 SER ( 94-) A O <-> 96 PHE ( 96-) A N 0.25 2.45 INTRA BL 94 SER ( 94-) A C <-> 96 PHE ( 96-) A N 0.21 2.69 INTRA BL 197 LYS ( 197-) A NZ <-> 218 GLU ( 218-) A OE2 0.19 2.51 INTRA BL 202 ASN ( 202-) A O <-> 206 LYS ( 206-) A N 0.14 2.56 INTRA BL 122 ASN ( 122-) A O <-> 123 SER ( 123-) A C 0.13 2.47 INTRA BF 196 ALA ( 196-) A O <-> 199 ALA ( 199-) A N 0.11 2.59 INTRA BL 196 ALA ( 196-) A O <-> 200 ILE ( 200-) A N 0.10 2.60 INTRA BL 200 ILE ( 200-) A CG2 <-> 216 PHE ( 216-) A CZ 0.09 3.11 INTRA BL 109 ILE ( 109-) A O <-> 116 GLY ( 116-) A N 0.07 2.63 INTRA BL 85 PRO ( 85-) A O <-> 88 ILE ( 88-) A N 0.06 2.64 INTRA BF 175 ARG ( 175-) A C <-> 176 ASN ( 176-) A CG 0.04 3.06 INTRA BF 14 GLY ( 14-) A O <-> 21 PHE ( 21-) A N 0.03 2.67 INTRA BF 13 ASP ( 13-) A N <-> 142 ARG ( 142-) A O 0.03 2.67 INTRA BF 116 GLY ( 116-) A CA <-> 130 PHE ( 130-) A CD1 0.03 3.17 INTRA BL 177 GLY ( 177-) A O <-> 212 GLU ( 212-) A N 0.03 2.67 INTRA BL 15 TYR ( 15-) A N <-> 140 LYS ( 140-) A O 0.02 2.68 INTRA BF 109 ILE ( 109-) A N <-> 116 GLY ( 116-) A O 0.02 2.68 INTRA BL 159 ILE ( 159-) A O <-> 162 MET ( 162-) A N 0.02 2.68 INTRA BL 36 ASN ( 36-) A C <-> 38 ALA ( 38-) A N 0.02 2.88 INTRA BF 13 ASP ( 13-) A O <-> 142 ARG ( 142-) A N 0.01 2.69 INTRA BF 8 VAL ( 8-) A N <-> 46 ILE ( 46-) A O 0.01 2.69 INTRA BF 97 THR ( 97-) A C <-> 99 ARG ( 99-) A N 0.01 2.89 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.
222 ARG ( 222-) A -9.01 83 ARG ( 83-) A -7.27 175 ARG ( 175-) A -6.69 40 ILE ( 40-) A -5.79 220 PHE ( 220-) A -5.72 221 GLU ( 221-) A -5.71 35 TYR ( 35-) A -5.31 207 ARG ( 207-) A -5.29 52 GLN ( 52-) A -5.16 189 PHE ( 189-) A -5.07 82 LYS ( 82-) A -5.03
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
220 PHE ( 220-) A 222 - ARG 222- ( A) -6.81
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: HIS, ASN, GLN side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favourable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. Be aware,
though, that if the topology could not be determined for one or more
ligands, then this option will make errors.
52 GLN ( 52-) 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.
12 TYR ( 12-) A N 47 PHE ( 47-) A N 52 GLN ( 52-) A N 53 VAL ( 53-) A N 66 VAL ( 66-) A N 77 GLU ( 77-) A N 83 ARG ( 83-) A N 96 PHE ( 96-) A N 104 ILE ( 104-) A N 122 ASN ( 122-) A ND2 134 LEU ( 134-) A N 151 ASP ( 151-) A N 166 ARG ( 166-) A N 176 ASN ( 176-) A N 178 THR ( 178-) A N 194 GLN ( 194-) A NE2 197 LYS ( 197-) A NZ 207 ARG ( 207-) A NE 209 GLU ( 209-) A N 211 ALA ( 211-) A N 219 THR ( 219-) 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.
122 ASN ( 122-) A OD1 194 GLN ( 194-) A OE1
13 ASP ( 13-) A H-bonding suggests Asn; but Alt-Rotamer 32 GLU ( 32-) A H-bonding suggests Gln 63 GLU ( 63-) 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 : -1.673 2nd generation packing quality : -0.589 Ramachandran plot appearance : -3.940 (poor) chi-1/chi-2 rotamer normality : -4.999 (bad) Backbone conformation : 0.620
Bond lengths : 0.430 (tight) Bond angles : 0.528 (tight) Omega angle restraints : 0.828 Side chain planarity : 0.287 (tight) Improper dihedral distribution : 0.559 B-factor distribution : 0.411 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 : 3.30
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : 1.3 Ramachandran plot appearance : -1.0 chi-1/chi-2 rotamer normality : -2.5 Backbone conformation : 1.6
Bond lengths : 0.430 (tight) Bond angles : 0.528 (tight) Omega angle restraints : 0.828 Side chain planarity : 0.287 (tight) Improper dihedral distribution : 0.559 B-factor distribution : 0.411 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.