OUTPUT Summary from CDPro:

PROTSS.OUT




OUTPUT from Each Program: (SELCON3, CDSSTR, and CONTINLL and CLUSTER)

SELCON3.OUT
 

Header details the references, and options (PRINT and IBASIS) selected. The selected reference set of proteins and types of secondary structure fractions obtained are indicated.

Input information along with the ordering of proteins in the reference set and initial guess is printed. The spectral and structural information is in BASIS file. Solution with all proteins in the basis set, corresponding to Hennessey and Johnson method, gives the helix content. Solutions with Sum_rule and Fraction _rule. Solution corresponds to original SELCON method. Solutions are screened using the third selection rule, Spectral_rule. Solutions correspond to SELCON2 protocol. The number of segments are also calculated based on the total helix content and the distorted helix content. Calculated spectra is compared with the experimental spectra. Solutions are screened using the fourth selection rule, Helix_rule. Solutions correspond to SELCON3 protocol.The number of segments are also calculated based on the total helix content and the distorted helix content.Calculated spectra is compared with the experimental spectra.
 Now the FOURTH SELECTION RULE is applied to the
 Solutions That SATISFY the first THREE rules.
 The HELIX FRACTION should be with in HLIMITS

 Hmin   .357 Hmax   .443 HelHJ   .425
 HELIX:   .434

 HLIMITS:    .404 --->   .464

   1   5   8  2   .244   .161   .061   .063   .181   .244   .953   .067
   2   6   9  1   .242   .167   .059   .064   .197   .255   .983   .066
   3   7   9  2   .247   .165   .060   .062   .185   .243   .964   .146
   4   8  10  1   .246   .173   .057   .061   .205   .268  1.010   .114
   .
   .
  31  38  28  1   .276   .164   .087   .062   .184   .256  1.029   .160
  32  40  29  1   .276   .164   .089   .063   .185   .258  1.035   .161
  33  41  30  1   .276   .164   .090   .064   .186   .261  1.041   .178

 Final Solution: Aver. of 33 Solns
 PROT   H(r)   H(d)   S(r)   S(d)   Trn    Unrd   SUM    RRcn
 TEST   .264   .167   .066   .061   .193   .263  1.015   .359

     +--------------------------------------------------+
     |  Based on the SOLUTION the Number of SEGMENTS of |
     |   HELICES (Per 100 Residues) are:     4.183      |
     |   STRANDS (Per 100 Residues) are:     3.067      |
     +--------------------------------------------------+
 

  For YOUR PROTEIN multiply No. of SEGMENTS by
  (Number of Residues) / 100
  e.g., If Number of Residues = 153,  Use a FACTOR of 1.53

  Average Length of Segments Remains as Estimated

     +--------------------------------------------------+
     |  Based on the SOLUTION Obtained                  |
     |   The AVERAGE LENGTH of HELICES :    10.311      |
     |   The AVERAGE LENGTH of STRANDS :     4.146      |
     +--------------------------------------------------+
 

The solution at the end of the final valid stage (If no solutions at the end of third stage, solution at the end of second stage is selected) is appended to PROTSS.OUT file, which looks like,
 SELCON3   IBasis=3  SStr:    .264    .167    .066    .061    .193    .263
The calculated CD spectra corresponding to the solution is also output in a text file (CALCCD.OUT) for importing into any grapics software.

CDSSTR.OUT

Header details the references, and options (PRINT and IBASIS) selected. The selected reference set of proteins and types of secondary structure fractions obtained are indicated. Input information is printed. AND Solution with all proteins in the basis set, corresponding to Hennessey and Johnson method, gives the helix content. Solutions from CDSSTR are selected from among the 400 valid solutions which satisfy the Sum_rule and Fraction_rule. These are obtained by selecting a minimal basis set of EIGHT proteins randomly selected from the reference set, and solving for the structure in the self-consistent formalism. The final solution will be the average of solutions that satisfy the Helix_rule.
Valid Solutions (combinations):
 Number  SComb  H(r)  H(d)  S(r)  S(d)  Trn   Unrd
  Hmin:   .44;  Hmax:   .50
       1     3   .29   .17   .16   .10   .12   .18
       2     4   .30   .15   .01   .07   .21   .27
       .
       .
       .

      91   394   .26   .19   .05   .07   .19   .27
      92   396   .29   .16  -.03   .06   .23   .24
      93   398   .30   .17   .11   .06   .12   .25

 Predicted:  H(r)= .29  H(d)= .18  S(r)= .06  S(d)= .06  Trn = .17  Unrd= .24

            isstr=400 icntf=  93
 
 

     +--------------------------------------------------+
     |  Based on the SOLUTION the Number of SEGMENTS of |
     |   HELICES (Per 100 Residues) are:     4.418      |
     |   STRANDS (Per 100 Residues) are:     3.235      |
     +--------------------------------------------------+
 

  For YOUR PROTEIN multiply No. of SEGMENTS by
  (Number of Residues) / 100
  e.g., If Number of Residues = 153,  Use a FACTOR of 1.53

  Average Length of Segments Remains as Estimated

     +--------------------------------------------------+
     |  Based on the SOLUTION Obtained                  |
     |   The AVERAGE LENGTH of HELICES :    10.453      |
     |   The AVERAGE LENGTH of STRANDS :     3.990      |
     +--------------------------------------------------+
 
 

The solution is appended to PROTSS.OUT file, which looks like,
 CDSSTR    IBasis=3  SStr:    .285    .177    .064    .065    .173    .240
The reconstructed CD spectra is output in a text file (RECONCD.OUT) for importing into any grapics software.


 

CONTINLL.OUT
 

Header details the references, and options (PRINT and IBASIS) selected. The selected reference set of proteins and types of secondary structure fractions obtained are indicated.

Input information along with the ordered list of proteins is printed. Oredered list of proteins in numbered and the corresponding spectral and structural information is in BASIS.PG file. Solution with all proteins in the basis set gives the helix content and solution corresponds to the original CONTIN method. CONTIN gives a list of solutions with varying values of regularizer and we have selected the solution with the least standard error as the best solution. The CONTIN selected solution, solution based on degrees of freedom are summarized in SUMMARY.PG and the complete CONTIN output can be generated using IPRINT option.


The variable selection is performed by removing the least similar protein (to the test protein) and the solutions that satisfy the Helix_rule are listed and averaged to get the final solution.

CONTIN gives a list of solutions with varying values of regularizer and we have selected the solution with the least standard error as the best solution. The CONTIN selected solution, solution based on degrees of freedom are summarized in SUMMARY.PG and the complete CONTIN output can be generated using IPRINT option. With IPRINT=0 only the final CONTIN output (with number of proteins = 6) will be in CONTIN.OUT.

The solution is appended to PROTSS.OUT file, which looks like,
 ContinLL  IBasis=3  SStr:    .256    .155    .064    .069    .184    .272
The file SUMMARY.PG contains the three solutions from CONTIN (1. CONTIN chosen solution, 2. Solution based on minimum degrees of freedom, and 3. Solution with minimum error) for all variable selection based reference sets. This looks like:
--------------------------------------------------------------------------------

    Number of Proteins: 36
 
 

[1] CONTIN-Chosen Solution;      ISol= 12   .37   .22   .19   .10   .08   .05
[2] Ave of  5 Solns with Deg Freed:  7-16   .26   .14   .07   .08   .18   .27
[3] Solution with Min. Error;    Isol=  9   .26   .15   .07   .08   .18   .27
--------------------------------------------------------------------------------

    Number of Proteins: 35
 
 

[1] CONTIN-Chosen Solution;      ISol= 12   .37   .22   .19   .10   .08   .05
[2] Ave of  5 Solns with Deg Freed:  7-16   .26   .14   .08   .08   .17   .26
[3] Solution with Min. Error;    Isol=  9   .26   .15   .08   .08   .18   .26
 

 .
 .
 .
 .
 .
    Number of Proteins:  7
 
 

[1] CONTIN-Chosen Solution;      ISol= 12   .24   .18   .08   .06   .17   .27
[2] Ave of 11 Solns with Deg Freed:  7-16   .21   .20   .08   .06   .15   .30
[3] Solution with Min. Error;    Isol= 11   .25   .17   .08   .06   .18   .26
--------------------------------------------------------------------------------

    Number of Proteins:  6
 
 

[1] CONTIN-Chosen Solution;      ISol= 12   .21   .18   .09   .07   .16   .29
[2] Ave of 11 Solns with Deg Freed:  7-16   .19   .20   .09   .06   .15   .32
[3] Solution with Min. Error;    Isol= 11   .21   .17   .09   .07   .18   .28
********************************************************************************
 



 

CLUSTER.OUT
 

Header details the references and the reference sets of proteins.

Input information is printed. OUTPUT: Position of the given CD spectrum w.r.t. each pair of classes. + indicates the assignment.


Predicted class and cration of class specific files.

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