CYANA Macro: overview: Difference between revisions
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Revision as of 13:40, 31 July 2011
Parameters
- file=filename.ovw
- (default: blank)
- structures=integer
- (default: 0)
- range=string
- (default: none)
- reference=string
- (default: blank)
- significant=integer
- (default: -1)
- hbond=integer
- (default: -1)
- mode=sum|average|rms
- (default: rms)
- ang
- cor
- pdb
- mean
- details
Description
Summarizes the results of a structure calculation. The summary is either stored in an overview file name.ovw, or shown on standard output. The selected structures are sorted with regard to their target function value and the given number of structures with the lowest target function values are analyzed and, if one or several of the options ang, cor or pdb are given, saved in an angle file name.ang, a DG format coordinate file name.cor, or a PDB coordinate file, name.pdb, respectively. The remaining structures are permanently discarded. The target function values are recalculated on the basis of the current restraints, weights and other parameters. The summary starts with a table of the target function values and restraint violation statistics:
Structural statistics:
str target upper limits van der Waals torsion angles
function # rms max # sum max # rms max
1 0.20 1 0.0035 0.20 0 1.4 0.16 0 0.1205 1.22
2 0.22 1 0.0036 0.19 0 1.5 0.17 0 0.1499 1.52
3 0.22 2 0.0039 0.19 0 1.4 0.16 0 0.1597 1.64
4 0.22 1 0.0032 0.18 0 1.5 0.16 0 0.1393 1.43
5 0.22 1 0.0037 0.20 0 1.5 0.16 0 0.1751 1.79
6 0.22 1 0.0036 0.19 0 1.6 0.16 0 0.1368 1.39
7 0.22 2 0.0041 0.21 0 1.4 0.16 0 0.1730 1.79
8 0.23 1 0.0034 0.18 0 1.6 0.16 0 0.1116 1.12
9 0.24 1 0.0037 0.19 0 1.6 0.17 0 0.1647 1.69
10 0.24 2 0.0039 0.18 0 1.6 0.16 0 0.1312 1.31
11 0.24 2 0.0038 0.18 0 1.7 0.16 0 0.1127 1.13
12 0.24 2 0.0041 0.18 0 1.6 0.16 0 0.1322 1.26
13 0.25 2 0.0038 0.18 0 1.6 0.16 0 0.1475 1.49
14 0.25 2 0.0042 0.21 0 1.6 0.17 0 0.1497 1.45
15 0.25 1 0.0037 0.20 0 1.8 0.16 0 0.1287 1.25
16 0.25 1 0.0033 0.18 0 1.8 0.16 0 0.1347 1.37
17 0.26 1 0.0035 0.18 0 1.8 0.16 0 0.1568 1.57
18 0.26 2 0.0039 0.19 0 1.8 0.16 0 0.1308 1.32
19 0.26 1 0.0040 0.20 0 1.9 0.16 0 0.1240 1.22
20 0.26 1 0.0033 0.18 0 1.7 0.16 0 0.1678 1.46
Ave 0.24 1 0.0037 0.19 0 1.6 0.16 0 0.1423 1.42
+/- 1.71E-02 0 0.0003 0.01 0 0.1 0.00 0 0.0188 0.20
Min 0.20 1 0.0032 0.18 0 1.4 0.16 0 0.1116 1.12
Max 0.26 2 0.0042 0.21 0 1.9 0.17 0 0.1751 1.79
Cut 0.10 0.20 5.00
This table has one row for each structure, containing the rank of the structure sorted by target function value, the target function value, and three columns for each type of conformational restraints that is present. For each restraint type, the first column gives the number of restraints that are violated by more than the cutoff value given in the last row (“Cut”), the root-mean-square (RMS) violation calculated over all, violated and fulfilled, restraints of this type, and the maximal violation. Depending on the mode, it is possible to report the sum of the violations or the average violations instead of the RMS violation. The five bottom lines of the Table give the average value, the standard deviation, the minimum value, and the maximum value of the corresponding quantity over the individual structures, as well as the cutoff value for significant violations. Restraints that are violated in a significant number of structures by more than the corresponding cutoff value are reported:
Constraints violated in 6 or more structures:
# mean max. 1 5 10 15 20
Upper H PHE 64 - HB2 GLU 65 5.50 11 0.11 0.21 +++ ++* + +++ + peak 3766
Upper H PHE 64 - HB3 GLU 65 5.50 9 0.08 0.19 + + ++++ +* + peak 3766
2 violated distance constraints.
0 violated angle constraints.
Each line identifies a violated restraint, and gives the number of structures in which the restraint is violated by more than the aforementioned cutoff value (column labeled “#”), its maximal violation (column “max.”), and the structures in which the violations occur (a one-character column for each structure that is analyzed). Structures in which the restraint is violated by more than the cutoff are marked with “+”, or with a “*” for the structure in which the maximal violation occurs. If available, the number of the cross peak from which the restraint originated is given at the end of the line. A list of the hydrogen bonds that occur in more than hbond structures is given if requested by the hbond parameter:
Hydrogen bonds: # 1 5 10 15 20 H LYS 23 - O SER 19 20 ++++++++++++++++++++ H ARG 24 - O TYR 20 19 ++++++++++++ +++++++ HE21 GLN 25 - O GLN 25 20 ++++++++++++++++++++ H LEU 26 - O GLU 22 20 ++++++++++++++++++++ H LEU 28 - O ARG 24 20 ++++++++++++++++++++ H ASN 31 - O SER 27 20 ++++++++++++++++++++ H ARG 40 - O LYS 37 15 +++ + +++++++ +++ + H VAL 41 - O LEU 38 20 ++++++++++++++++++++ H ILE 44 - O VAL 41 18 ++++ ++++++++++ ++++ H ARG 48 - O ILE 45 16 ++ ++++++++ ++++++ HH21 ARG 48 - OG SER 47 15 ++ + +++++ ++++ +++ H GLU 49 - O ILE 45 20 ++++++++++++++++++++ H LEU 52 - O GLU 49 20 ++++++++++++++++++++ H LYS 53 - O GLU 49 19 ++++++ +++++++++++++ H SER 55 - O LYS 53 15 +++++ + ++++++ + ++ H GLU 76 - O LEU 72 20 ++++++++++++++++++++ H VAL 79 - O LEU 75 17 ++++++++++++ + ++++ H THR 80 - O GLU 76 20 ++++++++++++++++++++ H CYS 82 - O TYR 78 15 +++++++++++ + + ++ H LEU 83 - O VAL 79 18 +++++ ++++++++++++ + 20 hydrogen bonds.
The number of structures in which a particular H-bond is found by the structures hbonds command is reported in the column labeled “#”, and the corresponding structures are identified by “+” signs. At the end of the overview RMSD values for the given residue range are given:
RMSDs for residues 15..84: Average backbone RMSD to mean : 0.37 +/- 0.08 A (0.22..0.53 A; 20 structures) Average heavy atom RMSD to mean : 0.80 +/- 0.09 A (0.66..1.00 A; 20 structures)
If the parameter range for residue range is absent, the range will be taken from the variable rmsdrange, if defined, or determined automatically by the overlay command otherwise. The RMSD calculation can be suppressed by setting range=–. The residue range used for the superposition is indicated, and RMSD values are computed for the backbone and heavy atoms with the rmsd command. The average value, the standard deviation, and the minimal and maximal values of the RMSDs between the analyzed structures and their mean coordinates are calculated. If a reference structure has been specified, then the RMSD values between the mean coordinates of the analyzed structures and the mean coordinates of the reference structure(s) are reported in two additional lines:
RMSDs for residues 15..84: Average backbone RMSD to mean : 0.37 +/- 0.08 A (0.22..0.53 A; 20 structures) Average heavy atom RMSD to mean : 0.80 +/- 0.09 A (0.66..1.00 A; 20 structures) Backbone RMSD to reference : 0.89 A (210 atoms) Heavy atom RMSD to reference : 1.17 A (571 atoms)
The number of corresponding atoms that have been superimposed in the two structures to calculate the RMSD values to the reference structure are given in parenthesis. RMSD values are computed with the rmsd command.
Additional output can be obtained by setting the option details. This includes first the consensus secondary structure determined by the DSSP algorithm (Kabsch & Sander, 1983), implemented in the command structures secondary:
Consensus secondary structure in 20 or more conformers:
1 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85
4-turn : >>>>XXXXXX<<<< >44>X4>XX><X<<4X444< >444< >444<>44>X>4XX<>X<4<<
3-turn : >33< >33< >33<>33<
Summary : HHHHHHHHHHHH HHHHHHHHH HHHHHHHHHHH
Sequence : GSSGSSGESEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRK
1 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85
A list of the torsion angles with a “split” distribution of values, determined by the command angles split, follows:
Split angles: mean1 mean2 dev # 1 5 10 15 20 PSI LYS 14 169.8 -61.6 11.0 4 + + + + CHI1 CYS 15 51.6 -65.4 9.5 10 ++ + + + + ++++ PSI PRO 17 124.5 173.6 0.6 6 ++ + + ++ PHI MET 18 -87.4 -132.4 3.5 6 ++ + + ++ CHI1 SER 19 -53.9 -168.9 11.6 8 ++ +++ ++ + CHI2 GLU 22 -75.8 -166.1 9.1 4 + + + + CHI2 LYS 32 -86.5 -176.9 3.7 2 + + CHI1 GLU 36 60.4 169.0 3.3 4 + + + + CHI1 VAL 42 70.4 -174.5 2.6 7 + + + +++ + CHI3 GLN 46 -23.5 21.6 4.4 4 + + + + CHI2 ARG 48 -68.8 -124.9 3.2 1 + CHI1 LYS 53 -175.2 74.4 7.4 5 ++ ++ + PSI LYS 53 -30.8 159.5 0.6 4 + + + + PHI ASN 54 -89.1 62.6 2.1 4 + + + + CHI1 GLU 61 -74.7 59.2 9.7 7 + + + + + ++ CHI1 GLU 65 83.2 -32.8 1.2 9 ++++ ++ + + + CHI1 THR 66 62.3 -175.9 8.8 9 + ++ + +++++ CHI2 LYS 68 168.0 75.9 10.4 7 ++ ++ +++ CHI1 ARG 73 -93.1 -159.1 8.2 10 ++ + +++ ++ ++ CHI2 ARG 73 -67.3 64.2 3.7 8 ++ + ++ + ++ CHI4 ARG 73 -179.8 76.8 9.1 6 ++ ++ + + CHI1 SER 81 -77.2 171.3 11.2 9 + ++ + + +++ + CHI1 CYS 82 -172.8 -78.5 11.7 9 + ++ + + ++ ++ PSI LYS 88 71.3 159.9 1.4 6 ++ + + + + 24 split dihedral angle distributions.
These are torsion angles for which the values in the analyzed structures are clearly clustered around two or more distinct positions. Split torsion angle values typically show up as “two conformations” in a visual representation of the 3D structure bundle, and may help to identify problems in the structure determination. Ramachandran plot outliers, i. e. amino acid residues with φ/ψ angle pairs in the generously allowed or disallowed regions of the PROCHECK Ramachandran plot (Laskowski et al., 1996) and the overall Ramachandran plot statistics are reported:
Ramachandran plot outliers:
# 1 5 10 15 20
LYS 88 1 ....* ... ....... ..
Residues in most favored regions : 89.1 %
Residues in additionally allowed regions: 10.8 % (symbol: .)
Residues in generously allowed regions : 0.0 % (symbol: +)
Residues in disallowed regions : 0.1 % (symbol: *)