Program : HETZE
Version : 970730
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : check quality of hetero entities
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-1999). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
970715 - 0.3 - first documented version
970730 - 0.4 - changed plane detection a trifle
This program checks the "quality" of hetero entities in PDB format.
It can be used to:
- check the quality of a ligand etc. obtained elsewhere before
including it in refinement
- get pointers as to which aspects of the structure's geometry
should be restrained during refinement (dihedrals, impropers,
flat planes)
- judge the quality of a ligand etc. after refinement
At present, the program will read a PDB file and scrutinise the first residue it encounters (irrespective of whether it comes on ATOM or HETATM cards). If there are multiple copies of this residue in the PDB file, the additional copies will be used to calculate statistics for bond lengths etc.
The program needs a library file which, at present, contains information regarding ideal lengths for a number of types of bond. (This may be extended in the future.)
The file may look as follows (note that the bond_type_code is ignored at present):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! ! hetze.lib-standard bond lengths for various types of bond ! ! Gerard J Kleywegt @ 970708 ! ! Version 0.1 @ 970708 ! ! Sources: ! - Handbook of Chemistry and Physics (75th edition) ! - Handbook of Chemistry and Physics (63rd edition) ! - FH Allen et al., J Chem Soc Perkin Trans II, S1-S19 (1987) ! ! BONDS ! ===== ! ! Element1 Element2 Bond_type_code Target_value Remark_string ! ' C' ' H' 1 1.09 'C-H range 1.056-1.115' ' C' 'Be' 1 1.93 'C-Be' ' C' 'Hg' 1 2.07 'C-Hg' ' C' ' B' 1 1.56 'C-B' ... ' O' ' P' 1 1.38 'O-P double' ' O' ' P' 2 1.63 'O-P single' ' O' ' S' 1 1.43 'O-S double' ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The first thing you need to supply is the name of the library file. If you have set up a local directory with library and database files for all Gerard's programs, and the environment GKLIB points to this directory, the program will automatically come up with the correct default name for this file. (In Uppsala: put the following into your .cshrc file: setenv GKLIB /nfs/public/lib)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----*** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE ***
Version - 970710/0.2 (C) 1992-97 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Tue Jul 15 16:41:24 1997 User - gerard Mode - interactive Host - sarek ProcID - 12374 Tty - /dev/ttyq28
*** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE ***
Reference(s) for this program:
* 1 * G.J. Kleywegt, Uppsala University, Uppsala, Sweden, Unpublished program.
For manuals and complete references, check: http://alpha2.bmc.uu.se/usf/
*** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE ***
Max nr of atoms : ( 250) Max nr of neighbours : ( 10) Max nr of bond types : ( 31250) Max nr of angle types : ( 62500) Max nr of dihedrals : ( 250) Max nr of impropers : ( 250) Max nr of library bonds : ( 500) Max nr of planes : ( 100) Max nr atoms per plane : ( 50)
Name of library file ? (/nfs/public/lib/hetze.lib) Reading library file Nr of library bonds read : ( 69) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The next required item is the name of your PDB file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supply the name of a PDB file containing your ligand or whatever. The *first* residue in the file will be processed All others will be used as extra example to get better bonds length, angle, etc. statistics ! Name of PDB file ? ( ) alf.pdb Name of PDB file : (alf.pdb) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Your PDB file should either contain *ALL* hydrogen atoms, or *NONE* of them. Tell the program which is the case:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Are *all* hydrogens in this file ? (N) Are *all* hydrogens in this file : (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Finally, if you want you can change the value of various program parameters, but this will usually not be necessary. In any event, the program will list the values it will use for these parameters.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Edit program parameters (Y/N) ? (N) nProgram parameters : Bond tolerance (A) : ( 0.450) Bond deviation tolerance (A) : ( 0.050) Large range for bond lengths (A) : ( 0.075) Large range for bond angles (d) : ( 8.000) Large range for dihedrals (d) : ( 10.000) Large range for impropers (d) : ( 8.000) Improper deviation tolerance (d) : ( 8.000) Flat improper cut-off (d) : ( 15.000) Max distance to a flat plane (A) : ( 0.200) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The program will read your PDB file, figure out which residue to scrutinise, and store any additional copies of the same residue type (provided they contain all atoms also contained in the original residue). If your PDB file contains a PDB FORMUL record, this will also be read (also if the formula is on a REMARK record as in the "hetero.pdb" file). This formula will also be used to verify atom types. For instance, if you have called your carbon atoms "AC1 " etc., the program would deduce that these are actinium, rather than carbon, atoms. However, if the formula was provided, the program will note that the compound does not contain any actinium, and will guess that the atom is really a carbon.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Reading PDB file ... Using residue : (MAN) Identifier : (A 503) Segment ID : ( ) Atom # 1 = C1 @ -0.041 48.314 51.297 1.00 97.46 Atom # 2 = C2 @ -0.688 48.942 52.525 1.00 97.46 Atom # 3 = C3 @ -1.689 47.975 53.150 1.00 97.46 Atom # 4 = C4 @ -2.700 47.509 52.106 1.00 97.46 Atom # 5 = C5 @ -1.979 46.908 50.901 1.00 97.46 Atom # 6 = C6 @ -2.966 46.527 49.799 1.00 97.46 Atom # 7 = O2 @ -1.335 50.144 52.168 1.00 97.46 Atom # 8 = O3 @ -2.358 48.597 54.224 1.00 97.46 Atom # 9 = O4 @ -3.563 46.548 52.673 1.00 97.46 Atom # 10 = O5 @ -1.043 47.861 50.374 1.00 97.46 Atom # 11 = O6 @ -2.285 46.326 48.577 1.00 97.46 Extra example ? (MAN A 504) Example OK # ( 1) Extra example ? (MAN A 505) Example OK # ( 2) ... Extra example ? (MAN B 509) Example OK # ( 13)Nr of atoms read : ( 11) Nr of extra examples : ( 13)
RMSD (all atoms) for example # 1 = 0.392 A RMSD (all atoms) for example # 2 = 0.539 A RMSD (all atoms) for example # 3 = 0.458 A RMSD (all atoms) for example # 4 = 0.100 A RMSD (all atoms) for example # 5 = 0.206 A RMSD (all atoms) for example # 6 = 0.550 A RMSD (all atoms) for example # 7 = 0.000 A RMSD (all atoms) for example # 8 = 0.392 A RMSD (all atoms) for example # 9 = 0.539 A RMSD (all atoms) for example # 10 = 0.458 A RMSD (all atoms) for example # 11 = 0.100 A RMSD (all atoms) for example # 12 = 0.206 A RMSD (all atoms) for example # 13 = 0.550 A
==> Deduced formula : (C 6 O 5) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If there are extra copies of the residue, the RMSD on all atoms will be listed for each copy (note that high values may be due to large variations in unrestrained conformational torsion angles).
The deduced chemical formula will be listed, along with the formula read from the file (if any).
In the next step, the program will try to figure out which atoms are bonded. Two atoms are bonded if their distance does not exceed the sum of their covalent bond radii plus a small tolerance (0.45 Å by default; the cut-off will be printed). If there are extra copies of the residue, the ESD, minimum and maximum lengths of this bond will also be listed, and a warning issued if the range is large. Finally, the program will look for examples of this type of bond in the library, and if there are any, it will list the type. If the length is far away from the ideal value, a warning will be printed.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Looking for bonded atoms ...Bond C1 - C2 = 1.523 A (cutoff : 1.810) ESD, Min, Max : 0.001 1.521 1.525 Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54
Bond C1 - O5 = 1.430 A (cutoff : 1.810) ESD, Min, Max : 0.004 1.422 1.436 Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single
...
Bond C6 - O6 = 1.412 A (cutoff : 1.810) ESD, Min, Max : 0.002 1.409 1.414 Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.02) For: C-O single
Nr of bonds found : ( 11) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The program will now generate a list of neighbour atoms for every atom. Also, if the PDB file did not contain all hydrogen atoms explicitly, the number of hydrogen atoms will be guesstimated by the program using the same simple algorithm as in XPLO2D.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Generating neighbour lists ...Trying to guess number of hydrogens ... Minimum C-C single bond (A) : ( 1.480) Minimum C-C double bond (A) : ( 1.280) Minimum C-N single bond (A) : ( 1.400) Minimum C-N double bond (A) : ( 1.200) Minimum C-O single bond (A) : ( 1.300) Minimum C-S single bond (A) : ( 1.770) Carbon C1 Nbrs: 2 ~Hs: 2 Carbon C2 Nbrs: 3 ~Hs: 1 Carbon C3 Nbrs: 3 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 1 Carbon C5 Nbrs: 3 ~Hs: 1 Carbon C6 Nbrs: 2 ~Hs: 2 Oxygen O2 Nbrs: 1 ~Hs: 1 Oxygen O3 Nbrs: 1 ~Hs: 1 Oxygen O4 Nbrs: 1 ~Hs: 1 Oxygen O5 Nbrs: 2 ~Hs: 0 Oxygen O6 Nbrs: 1 ~Hs: 1 Est. total nr of hydrogens : ( 12) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The program will generate all unique angles and list their values. If there were extra copies, the ESD, minimum and maximum value will also be listed. If the observed range of values is large, a warning message will be printed.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Looking for angles ...AtmJ AtmI AtmK <Angle> ESD Min Max Range ---- ---- ---- ------- --- --- --- ----- C2 C1 O5 109.76 0.53 108.90 110.64 1.74 C1 C2 C3 110.42 0.33 109.92 110.98 1.06 C1 C2 O2 109.94 0.19 109.73 110.35 0.62 C3 C2 O2 109.88 0.19 109.51 110.20 0.70 C2 C3 C4 110.54 0.29 110.26 111.20 0.93 C2 C3 O3 110.06 0.19 109.70 110.33 0.63 C4 C3 O3 109.79 0.17 109.45 110.04 0.59 C3 C4 C5 110.51 0.23 110.20 110.86 0.66 C3 C4 O4 109.82 0.11 109.63 109.98 0.35 C5 C4 O4 109.74 0.16 109.43 110.01 0.58 C4 C5 C6 111.19 0.17 110.82 111.38 0.56 C4 C5 O5 109.33 0.27 108.90 109.72 0.81 C6 C5 O5 108.94 0.26 108.46 109.27 0.80 C5 C6 O6 110.21 0.17 109.87 110.36 0.48 C1 O5 C5 114.46 0.50 113.98 115.37 1.39 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Next, the program will define all dihedral angles it can detect. Again, statistics are listed if there are extra copies. Note that a large range for a dihedral could point to a free, conformational torsion. If the (average) dihedral is close to 0 or 180 degrees, the program will guess that the related atoms should be "flat".
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Looking for dihedrals ...AtmK AtmI AtmJ AtmL <Dihedral> Min Max Range ---- ---- ---- ---- --------- --- --- ----- O5 C1 C2 C3 55.29 53.92 57.71 3.78 O5 C1 C2 O2 -66.12 -67.91 -63.33 4.58 C2 C1 O5 C5 -61.03 -64.06 -57.87 6.19 C1 C2 C3 C4 -52.89 -54.50 -50.44 4.06 C1 C2 C3 O3 -174.33 -176.13 -171.67 4.47 Flat ? O2 C2 C3 C4 68.56 66.62 70.99 4.36 O2 C2 C3 O3 -52.89 -55.01 -50.24 4.77 C2 C3 C4 C5 53.04 50.09 55.00 4.92 C2 C3 C4 O4 174.25 171.20 176.06 4.86 Flat ? O3 C3 C4 C5 174.64 171.47 176.67 5.20 Flat ? O3 C3 C4 O4 -64.14 -67.45 -62.28 5.17 C3 C4 C5 C6 -175.66 -177.24 -173.55 3.69 Flat ? C3 C4 C5 O5 -55.34 -56.66 -53.64 3.02 O4 C4 C5 C6 63.09 61.51 65.11 3.59 O4 C4 C5 O5 -176.59 -177.89 -174.99 2.90 Flat ? C4 C5 C6 O6 141.67 50.86 238.04 172.82 >>> WARNING - large range for previous dihedral ! O5 C5 C6 O6 20.95 -69.32 117.51 173.17 >>> WARNING - large range for previous dihedral ! C4 C5 O5 C1 60.88 58.40 63.62 5.22 C6 C5 O5 C1 -177.43 -179.77 -174.73 5.04 Flat ? ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Every atom with 3 or more neighbours gives rise to an improper. If the atom and its neighbours are flat, this improper should be zero; if they are terahedral, the improper should be +35 or -35 degrees. If impropers do not have a value near any of these three, a warning is issued. Also, if the range of observed values is large, a warning message is printed.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Looking for impropers (and planes) ...Atm* Nbr1 Nbr2 Nbr3 <Improper> Min Max Range ---- ---- ---- ---- --------- --- --- ----- C2 C1 C3 O2 33.47 32.97 33.73 0.76 C3 C2 C4 O3 33.41 33.20 33.72 0.52 C4 C3 C5 O4 -33.61 -33.77 -33.50 0.26 C5 C4 C6 O5 -34.56 -34.69 -34.43 0.26 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When it looks for impropers, the program starts a list of atoms which might be part of planar groups. Subsequently, it will look for any other sets of atoms that might be part of planar groups. For all the potential planes found, the program then starts looking for any other atoms which might also be in this plane (and which are bonded to at least one atom already in the plane). Finally, planes which are copies or subsets of other planes are removed. The remaining planes and their atoms are listed, along with the RMSD to the least-squares plane and the distance of each atom to that plane. (The plane analysis only uses the coordinates of the first copy of the compound !)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Number of possible flat planes : ( 0)Looking for more planes ...
Number of possible flat planes : ( 1)
Expanding planes ...
Removing non-unique planes ...
Plane nr : ( 1) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) O5 -0.002 C1 0.002 C5 -0.001 C6 0.001 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Finally, a summary is printed.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ------------------------ ----- SUMMARY ----- -------------------
Residue type : (MAN) Identifier : (A 503) Segment ID : ( )
Nr of atoms : ( 11) Deduced formula : (C 6 O 5) Guestimated total nr of Hs : ( 12) Nr of extra examples : ( 13)
Nr of bonds found : ( 11) ... bonds with large ranges : ( 0) -"- % : ( 0.000) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 11) ... bonds far from ideal value : ( 0) -"- % : ( 0.000)
Nr of angles found : ( 15) ... angles with large ranges : ( 0) -"- % : ( 0.000)
Nr of dihedrals found : ( 19)
Nr of atoms with impropers : ( 4) ... imprs with large ranges : ( 0) -"- % : ( 0.000) ... imprs far from ideal value : ( 0) -"- % : ( 0.000)
Nr of flat planes : ( 1)
All done ...
*** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE ***
Version - 970710/0.2 Started - Tue Jul 15 16:45:28 1997 Stopped - Tue Jul 15 16:45:32 1997
CPU-time taken : User - 0.1 Sys - 0.0 Total - 0.1
*** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE ***
>>>>>> This program: (C) 1992-97, GJ Kleywegt & TA Jones <<<<<< >>>> E-mail: gerard@xray.bmc.uu.se or alwyn@xray.bmc.uu.se <<<< > http://alpha2.bmc.uu.se/usf/gerard_manuals.html <
*** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE *** HETZE ***
STOP ... Toodle pip ... statement executed ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The variety of hetero compounds is enormous compared to that of the amino acids and nucleic acids. Therefore, a geometry-checking program is mor edifficult to make for these compounds. One test to see if it doesn't give too many false positives (i.e., things which are flagged as error/outlier/warning, while they are correct) is to run it on a set of protein residues from a high-resolution structure. Below is the result for all tryptophan residues taken from PDB entry 1CEL (cellobiohydrolase I at 1.8 Å):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Looking for angles ...AtmJ AtmI AtmK <Angle> ESD Min Max Range ---- ---- ---- ------- --- --- --- ----- N CA C 111.24 3.15 105.67 115.67 9.99 >>> WARNING - large range for previous angle ! N CA CB 109.92 1.55 106.16 111.88 5.72 C CA CB 109.46 1.92 105.35 113.39 8.04 >>> WARNING - large range for previous angle ! CA C O 120.82 0.56 119.66 121.62 1.95 CA CB CG 114.73 1.23 113.04 117.05 4.01 ... Looking for impropers (and planes) ...
Atm* Nbr1 Nbr2 Nbr3 <Improper> Min Max Range ---- ---- ---- ---- --------- --- --- ----- CA N C CB 34.95 32.19 37.35 5.17 CG CB CD1 CD2 0.14 -4.46 2.85 7.32 CD2 CG CE2 CE3 0.01 -0.29 0.15 0.44 CE2 CD2 NE1 CZ2 0.01 -0.10 0.13 0.23 ... ------------------- ----- SUMMARY ----- -------------------
Residue type : (TRP) Identifier : (A 16) Segment ID : (1CEL)
Nr of atoms : ( 14) Deduced formula : (C 11 N 2 O 1) Guestimated total nr of Hs : ( 11) Nr of extra examples : ( 17)
Nr of bonds found : ( 15) ... bonds with large ranges : ( 0) -"- % : ( 0.000) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 15) ... bonds far from ideal value : ( 0) -"- % : ( 0.000)
Nr of angles found : ( 20) ... angles with large ranges : ( 2) -"- % : ( 10.000)
Nr of dihedrals found : ( 26)
Nr of atoms with impropers : ( 4) ... imprs with large ranges : ( 0) -"- % : ( 0.000) ... imprs far from ideal value : ( 0) -"- % : ( 0.000)
Nr of flat planes : ( 2) ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that all bond lengths are okay (even though HETZE knows nothing about the Engh & Huber parameters, and uses a rather broad classification). The largest angle variations occur for TAU(N-CA-C), which actually depends upon the secondary structure. No angle has a range exceding 10 degrees. All impropers are in order. This indicates that the conservative checks that the program carries out are justified, and that one should worry if one gets lots of warning messages.
A single copy of this ion was used, so no statistics will be printed regarding ranges of bond lengths etc. The formula was included. There are no ideal Al-F bond lengths in the library. The entire group is planar.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Nr of atoms read : ( 5) Nr of extra examples : ( 0)==> List of elements : ( AL1 F4 1-) ==> Deduced formula : (F 4 AL 1)
Looking for bonded atoms ...
Bond AL - F1 = 1.788 A (cutoff : 2.440) Nr of entries in library : ( 0)
...
Est. total nr of hydrogens : ( 0)
Looking for angles ...
AtmJ AtmI AtmK Angle ---- ---- ---- ----- F1 AL F2 178.80 F1 AL F3 90.41 F1 AL F4 90.04 F2 AL F3 89.86 F2 AL F4 89.65 F3 AL F4 178.31
Looking for dihedrals ...
AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- -------
Looking for impropers (and planes) ...
Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- --- Atom with 4 or more non-H neighbours --- AL F1 F3 F2 -0.83 AL F2 F3 F4 1.15 AL F3 F1 F4 1.15 AL F4 F1 F2 -0.82
Number of possible flat planes : ( 4)
Looking for more planes ...
Number of possible flat planes : ( 4)
Expanding planes ...
Removing non-unique planes ... Plane 1 is a subset of plane 2 Plane 2 is a subset of plane 4 Plane 3 is a subset of plane 4
Plane nr : ( 4) Nr of atoms : ( 5) RMSD to least-squares plane (A): ( 0.009) Atom Dist (A) AL 0.017 F4 -0.008 F1 -0.001 F2 -0.001 F3 -0.008 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This used 12 FAD copies from structures refined to 2.0 Å resolution or better. Note that even at these resolutions, the geometry of the compound varies enormously, and several copies contain errors.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... ==> List of elements : ( C27 H33 N9 O15 P2) ==> Deduced formula : (C 27 N 9 O 15 P 2)Looking for bonded atoms ...
Bond AP - AO1 = 1.482 A (cutoff : 2.180) ESD, Min, Max : 0.038 1.453 1.602 >>> WARNING - Large variation in previous bond length : ( 0.149) Nr of entries in library : ( 2) >>> WARNING - Too far from ideal 1.38 (devn. 0.10) For: O-P double ... Bond C4 - C4A = 1.460 A (cutoff : 1.810) ESD, Min, Max : 0.029 1.388 1.514 >>> WARNING - Large variation in previous bond length : ( 0.127) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.02) For: C-C single shortened; range 1.421-1.46 ... Bond C5* - O5* = 1.489 A (cutoff : 1.810) ESD, Min, Max : 0.069 1.406 1.647 >>> WARNING - Large variation in previous bond length : ( 0.241) Nr of entries in library : ( 5) Closest to 1.47 (devn. 0.02) For: C-O single strained ... Est. total nr of hydrogens : ( 38)
Looking for angles ...
AtmJ AtmI AtmK <Angle> ESD Min Max Range ---- ---- ---- ------- --- --- --- ----- AO1 AP AO2 119.99 3.36 115.18 125.67 10.49 >>> WARNING - large range for previous angle ! AO1 AP AO5* 106.23 3.24 97.56 110.66 13.11 >>> WARNING - large range for previous angle ! AO1 AP O3 109.05 3.16 103.66 114.34 10.68 >>> WARNING - large range for previous angle ! AO2 AP AO5* 105.89 4.29 93.94 112.77 18.84 >>> WARNING - large range for previous angle ! AO2 AP O3 111.29 4.68 105.16 118.91 13.76 >>> WARNING - large range for previous angle ! AO5* AP O3 102.08 4.31 92.65 106.87 14.21 >>> WARNING - large range for previous angle ! AP AO5* AC5* 119.83 4.73 110.49 125.02 14.54 >>> WARNING - large range for previous angle ! AO5* AC5* AC4* 106.21 2.86 98.84 110.06 11.22 >>> WARNING - large range for previous angle ! AC5* AC4* AO4* 108.62 2.18 103.63 111.20 7.57 AC5* AC4* AC3* 114.75 3.41 110.09 119.93 9.84 >>> WARNING - large range for previous angle ! AO4* AC4* AC3* 106.03 2.23 101.46 109.36 7.89 AC4* AO4* AC1* 106.61 1.39 104.98 109.28 4.30 ... Looking for dihedrals ...
AtmK AtmI AtmJ AtmL <Dihedral> Min Max Range ---- ---- ---- ---- --------- --- --- ----- AO1 AP AO5* AC5* -56.52 -177.88 -21.02 156.86 >>> WARNING - large range for previous dihedral ! AO2 AP AO5* AC5* -164.80 173.02 319.73 146.71 >>> WARNING - large range for previous dihedral ! ... AC1* AN9 AC8 AN7 -173.05 -177.33 -159.78 17.55 Flat ? >>> WARNING - large range for previous dihedral ! AC4 AN9 AC8 AN7 1.07 -3.06 7.10 10.16 Flat ? >>> WARNING - large range for previous dihedral ! AC1* AN9 AC4 AC5 173.79 161.77 182.25 20.48 Flat ? >>> WARNING - large range for previous dihedral ! AC1* AN9 AC4 AN3 -6.08 -15.75 -0.15 15.60 Flat ? >>> WARNING - large range for previous dihedral ! AC8 AN9 AC4 AC5 -0.49 -4.51 4.00 8.51 Flat ? AC8 AN9 AC4 AN3 179.64 176.32 185.45 9.13 Flat ? AN9 AC8 AN7 AC5 -1.12 -9.32 1.82 11.14 Flat ? >>> WARNING - large range for previous dihedral ! ... Looking for impropers (and planes) ...
Atm* Nbr1 Nbr2 Nbr3 <Improper> Min Max Range ---- ---- ---- ---- --------- --- --- ----- --- Atom with 4 or more non-H neighbours --- AP AO1 AO2 AO5* 28.75 -39.90 49.19 89.10 >>> WARNING - large range for previous improper ! AP AO2 AO5* O3 -28.10 -48.27 43.90 92.17 >>> WARNING - large range for previous improper ! AP AO5* O3 AO1 27.30 -36.67 41.70 78.38 >>> WARNING - large range for previous improper ! AP O3 AO1 AO2 -16.95 -28.72 29.87 58.59 >>> WARNING - large range for previous improper ! >>> WARNING - previous improper not near 0 or +/-35 !
AC4* AC5* AO4* AC3* -34.52 -37.34 -31.69 5.65 AC3* AC4* AO3* AC2* -36.70 -41.44 -32.62 8.82 >>> WARNING - large range for previous improper ! AC2* AC3* AO2* AC1* -40.62 -44.65 -37.28 7.37 AC1* AO4* AC2* AN9 34.78 31.21 37.49 6.28 ... ------------------- ----- SUMMARY ----- -------------------
Residue type : (FAD) Identifier : (X 1) Segment ID : ( )
Nr of atoms : ( 53) List of elements (from file) : ( C27 H33 N9 O15 P2) Deduced formula : (C 27 N 9 O 15 P 2) Guestimated total nr of Hs : ( 38) Nr of extra examples : ( 11)
Nr of bonds found : ( 58) ... bonds with large ranges : ( 25) -"- % : ( 43.103) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 52) ... bonds far from ideal value : ( 6) -"- % : ( 10.345)
Nr of angles found : ( 89) ... angles with large ranges : ( 31) -"- % : ( 34.831)
Nr of dihedrals found : ( 117)
Nr of atoms with impropers : ( 22) ... imprs with large ranges : ( 15) -"- % : ( 68.182) ... imprs far from ideal value : ( 1) -"- % : ( 4.545)
Nr of flat planes : ( 5) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present ("peppar, peppar").
Does not compute.
Created at Fri Dec 18 19:42:11 1998
by MAN2HTML version 971024/1.6