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.
258 CMH ( 206-) A - Atom types 261 ZYX ( 301-) A - OK
Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.
251 GLN ( 255-) A -
In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.
31 ILE ( 33-) A - 251 GLN ( 255-) 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: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
1 HIS ( 3-) A High
Obviously, the temperature at which the X-ray data was collected has some importance too:
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: 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 128 PHE ( 131-) A
RMS Z-score for bond lengths: 0.622
RMS-deviation in bond distances: 0.013
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.
1 HIS ( 3-) A CA CB CG 109.66 -4.1 1 HIS ( 3-) A CG ND1 CE1 110.08 4.5 2 HIS ( 4-) A CA C O 127.77 4.1 2 HIS ( 4-) A CA CB CG 119.00 5.2 2 HIS ( 4-) A CG ND1 CE1 112.55 6.9 2 HIS ( 4-) A CB CG CD2 136.00 5.3 13 HIS ( 15-) A CG ND1 CE1 118.40 12.8 13 HIS ( 15-) A ND1 CE1 NE2 102.60 -7.0 13 HIS ( 15-) A CD2 CG ND1 98.97 -7.1 13 HIS ( 15-) A CB CG CD2 135.45 4.9 32 ASP ( 34-) A CA CB CG 108.30 -4.3 34 HIS ( 36-) A CA CB CG 108.97 -4.8 41 SER ( 43-) A -O -C N 116.49 -4.1 60 ASN ( 62-) A CB CG ND2 104.67 -7.8 60 ASN ( 62-) A ND2 CG OD1 127.81 5.2 65 ASN ( 67-) A CA CB CG 118.36 5.8 72 GLN ( 74-) A CA C O 112.70 -4.8 72 GLN ( 74-) A NE2 CD OE1 128.75 6.1 75 ALA ( 77-) A -C N CA 129.66 4.4 83 ASP ( 85-) A CA CB CG 116.61 4.0 91 PHE ( 93-) A CA CB CG 118.34 4.5 94 HIS ( 96-) A NE2 CD2 CG 110.60 4.1 98 LEU ( 100-) A -C N CA 129.39 4.3 105 HIS ( 107-) A NE2 CD2 CG 110.50 4.0 127 ASP ( 130-) A CA CB CG 119.85 7.3 127 ASP ( 130-) A OD2 CG OD1 113.29 -4.0 133 GLN ( 136-) A NE2 CD OE1 127.37 4.8 176 PHE ( 179-) A CA CB CG 109.20 -4.6 187 ASP ( 190-) A -O -C N 111.92 -6.9 187 ASP ( 190-) A -C N CA 133.66 6.6 187 ASP ( 190-) A CA CB CG 116.67 4.1 226 ASN ( 230-) A CA CB CG 118.51 5.9 227 PHE ( 231-) A CA CB CG 120.81 7.0 235 GLU ( 239-) A CA CB CG 124.20 5.1 257 LYS ( 261-) A CA C O 113.80 -4.1
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 PHE ( 176-) A -2.2 199 PRO ( 202-) A -2.1 160 VAL ( 163-) A -2.1 164 ILE ( 167-) A -2.1 81 PRO ( 83-) A -2.0 148 GLY ( 151-) A -2.0 90 GLN ( 92-) 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.
27 SER ( 29-) A PRO omega poor 55 LEU ( 57-) A omega poor 73 ASP ( 75-) A Poor phi/psi 90 GLN ( 92-) A omega poor 109 LYS ( 111-) A Poor phi/psi 125 TYR ( 128-) A omega poor 175 ASN ( 178-) A Poor phi/psi 188 TYR ( 191-) A omega poor 194 SER ( 197-) A omega poor 198 PRO ( 201-) A PRO omega poor 200 LEU ( 203-) A Poor phi/psi 211 PRO ( 215-) A omega poor 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.390
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 13 HIS ( 15-) A 0 14 TRP ( 16-) A 0 17 ASP ( 19-) A 0 18 PHE ( 20-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 26 GLN ( 28-) A 0 27 SER ( 29-) A 0 36 ALA ( 38-) A 0 43 LYS ( 45-) A 0 48 SER ( 50-) A 0 51 GLN ( 53-) A 0 52 ALA ( 54-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) 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 0And so on for a total of 122 lines.
40 PRO ( 42-) A 0.06 LOW
19 PRO ( 21-) A -117.7 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.
8 HIS ( 10-) A ND1 <-> 262 HOH ( 645 ) A O 0.21 2.49 INTRA 124 LYS ( 127-) A NZ <-> 262 HOH ( 530 ) A O 0.20 2.50 INTRA 43 LYS ( 45-) A NZ <-> 262 HOH ( 669 ) A O 0.17 2.53 INTRA BF 16 LYS ( 18-) A NZ <-> 262 HOH ( 468 ) A O 0.15 2.55 INTRA 39 ASP ( 41-) A OD1 <-> 41 SER ( 43-) A N 0.14 2.56 INTRA BF 156 LYS ( 159-) A NZ <-> 262 HOH ( 587 ) A O 0.14 2.56 INTRA BF 43 LYS ( 45-) A O <-> 262 HOH ( 454 ) A O 0.12 2.28 INTRA 134 GLN ( 137-) A NE2 <-> 262 HOH ( 583 ) A O 0.12 2.58 INTRA 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.11 2.59 INTRA BL 38 TYR ( 40-) A O <-> 262 HOH ( 621 ) A O 0.10 2.30 INTRA 111 LYS ( 113-) A NZ <-> 262 HOH ( 667 ) A O 0.08 2.62 INTRA 172 ASP ( 175-) A OD1 <-> 262 HOH ( 607 ) A O 0.07 2.33 INTRA 1 HIS ( 3-) A N <-> 262 HOH ( 647 ) A O 0.06 2.64 INTRA BF 258 CMH ( 206-) A AHG <-> 262 HOH ( 487 ) A O 0.05 2.75 INTRA 248 LYS ( 252-) A NZ <-> 262 HOH ( 617 ) A O 0.05 2.65 INTRA 151 LYS ( 154-) A NZ <-> 262 HOH ( 592 ) A O 0.04 2.66 INTRA 210 GLU ( 214-) A OE2 <-> 262 HOH ( 494 ) A O 0.03 2.37 INTRA 34 HIS ( 36-) A A CD2 <-> 262 HOH ( 568 ) A O 0.01 2.79 INTRA 43 LYS ( 45-) A CE <-> 262 HOH ( 669 ) A O 0.01 2.79 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.
8 HIS ( 10-) A -6.24 98 LEU ( 100-) A -5.27 2 HIS ( 4-) A -5.20 133 GLN ( 136-) A -5.08
Chain identifier: A
Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
124 LYS ( 127-) A -3.12
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.
262 HOH ( 620 ) A O Unrecognized bound group for 202 Bound atom= 258 CMH ( 206-) A N
1 HIS ( 3-) A 134 GLN ( 137-) 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 65 ASN ( 67-) A ND2 98 LEU ( 100-) A N 138 LEU ( 141-) A N 166 THR ( 169-) A N 179 ARG ( 182-) A NH2 197 THR ( 200-) A N 201 LEU ( 204-) A N 226 ASN ( 230-) A ND2 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 256 PHE ( 260-) A N 260 GOL ( 311-) A O2 Only metal coordination for 92 HIS ( 94-) A NE2 Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.
262 HOH ( 445 ) A O 0.92 K 4 262 HOH ( 520 ) A O 1.13 K 4 H2O-B 262 HOH ( 549 ) A O 0.94 K 4 Ion-B 262 HOH ( 561 ) A O 0.97 K 5 Ion-B
159 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 : -0.145 2nd generation packing quality : 0.880 Ramachandran plot appearance : -0.744 chi-1/chi-2 rotamer normality : 0.390 Backbone conformation : -0.973
Bond lengths : 0.622 (tight) Bond angles : 1.246 Omega angle restraints : 1.131 Side chain planarity : 1.045 Improper dihedral distribution : 0.840 B-factor distribution : 0.969 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 : 1.20
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.1 Ramachandran plot appearance : -1.1 chi-1/chi-2 rotamer normality : -0.1 Backbone conformation : -1.2
Bond lengths : 0.622 (tight) Bond angles : 1.246 Omega angle restraints : 1.131 Side chain planarity : 1.045 Improper dihedral distribution : 0.840 B-factor distribution : 0.969 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.