CYANA Macro: overview

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 with the name given by the file parameter, 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 by more than the corresponding cutoff value in a significant number of structures, as defined by the significant parameter (default: 1/3 of the structures), 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. This table is also produced if the option details is set (see below). In this case the number of structures in which a hydrogen bond must be present in order to be reported defaults to the value of the parameter significant, or, if not given, to 1/3 of the structures.

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 determined by the command angles ramachandran 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: *)