openf5___> 11,OLD,SEQ,FORM, /sali/sali/sali/bin/modeller5o/modlib/top.ini
TOP______> TOP initialized.

                        MODELLER 5o, August 18, 1998            

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

                                                    v            
                      Copyright(c) 1989-1998 Andrej Sali         
                             All Rights Reserved                 

                                     v                           
                       Written by A. Sali, R. Sanchez,           
                   A. Badretdinov, A. Fiser & E. Feyfant         
                   Rockefeller University, New York, USA         
                     Harvard University, Cambridge, USA          
                 Imperial Cancer Research Fund, London, UK       
             Birkbeck College, University of London, London, UK  


Maximum number of protein chains (segments)      :     20
Maximum number of explicitly excluded atom pairs :    100
Maximum number of pseudo atoms                   :    200
Maximum optimization schedule length             :     50
Precision, host type, host name                  : single, r10000, poppy
Date and time of compilation                     : Tue Sep 15 12:15:20 EDT 1998  
Job starting time (YY/MM/DD  HH:MM:SS)           : 1998/09/16  14:34:15

 
 
iatmcls_W> MODEL atom not classified: GLY:OT1        
iatmcls_W> MODEL atom not classified: GLY:OT2        
 
 
iatmcls_W> MODEL atom not classified: GLY:OT1        
iatmcls_W> MODEL atom not classified: GLY:OT2        
 
 
iatmcls_W> MODEL atom not classified: GLY:OT1        
iatmcls_W> MODEL atom not classified: GLY:OT2        
 
 
iatmcls_W> MODEL atom not classified: GLY:OT1        
iatmcls_W> MODEL atom not classified: GLY:OT2        
defsym___> New number of symmetry segments, atom pairs:      1    25
defsym___> New number of symmetry segments, atom pairs:      2    50
defsym___> New number of symmetry segments, atom pairs:      3    75
defsym___> New number of symmetry segments, atom pairs:      4   150


>> ENERGY; Differences between the model's features and restraints:
chkcsp__W> no fixed restraints selected,
           there may be some dynamic ones.
chkcsp__W> you probably did not read the csrs file!
chkcmb__W> none of the needed non-bonded terms selected


ID1, ID2                                          :       1      1
Number of static restraints [all, selected]       :       0      0
Numb of non-bonded pairs                          :       0
Distance cutoff for non-bonded pairs search [A]   :        4.00000
Residue span range                                :       0  99999
Value of -Ln(Molecular pdf)                       :    0.11026E+06
Value of the symmetry term within -Ln(Mpdf)       :    0.11026E+06
Standard deviation for sphere overla (SPHERE_STDV):        0.05000
Radii factor (RADII_FACTOR)                       :        0.82000



Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   NUMVP   ... number of restraints with violation of PDF value > VIOL_REPORT_CUT2[i].
   RMS_1   ... rms(feature,minimally violated basis restraint,NUMB).
   RMS_2   ... rms(feature,ideal value,NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :       0       0      0   0.000   0.000    0.000000       1.000
 2 Bond angle potential               :       0       0      0   0.000   0.000    0.000000       1.000
 3 Stereochemical cosine torsion poten:       0       0      0   0.000   0.000    0.000000       1.000
 4 Stereochemical improper torsion pot:       0       0      0   0.000   0.000    0.000000       1.000
 5 soft-sphere overlap restraints     :       0       0      0   0.000   0.000    0.000000       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000    0.000000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000    0.000000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000    0.000000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000    0.000000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000    0.000000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000    0.000000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000    0.000000       1.000
13 Mainchain Omega dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
14 Sidechain Chi_1 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
15 Sidechain Chi_2 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
16 Sidechain Chi_3 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
17 Sidechain Chi_4 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000    0.000000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000    0.000000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000    0.000000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000    0.000000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000    0.000000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000    0.000000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000    0.000000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000    0.000000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000    0.000000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000    0.000000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000    0.000000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000    0.000000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000    0.000000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000    0.000000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the ideal value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers and names of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the ideal value (global minimum).
   VIOL   ... difference from the ideal value.
   RVIOL  ... relative difference from the ideal value.


<< end of ENERGY.
chkcsp__W> no fixed restraints selected,
           there may be some dynamic ones.
chkcsp__W> you probably did not read the csrs file!
chkcmb__W> none of the needed non-bonded terms selected


Report on the conjugate gradients optimization: 


Structure optimized:
   numb of all residues         :       24
   numb of all real atoms       :      100
   numb of selected real atoms  :      100
   numb of all pseudo atoms     :        0
   numb of selected pseudo atoms:        0

Restraints used:
   numb of static restraints         :        0
   numb of selected static restraints:        0
   numb of non-bonded pairs          :        0

Dynamic pairs routine 2: NATMxNATM cell sorting.

Parameters used:
   type of the optimization method                :        1
   RESIDUE_SPAN_RANGE                             :        0   99999
   RESIDUE_SPAN_SIGN                              :        T
   min atm shift before contacts update           :     0.39
   max atm shift that signals convergence         :   0.0100
   max allowed number of iterations               :      300
   restr res span triggering NlogN contacts alg   :       15
   cell size for dynamic pairs search [A]         :   4.0000

Scaling parameters:
   schedule                                :        1
   vdW contacts stand dev                  :   0.0500
   1 Bond length potential                 :   1.0000
   2 Bond angle potential                  :   1.0000
   3 Stereochemical cosine torsion potenti :   1.0000
   4 Stereochemical improper torsion poten :   1.0000
   5 soft-sphere overlap restraints        :   1.0000
   6 Lennard-Jones 6-12 potential          :   1.0000
   7 Coulomb point-point electrostatic pot :   1.0000
   8 H-bonding potential                   :   1.0000
   9 Distance restraints 1 (CA-CA)         :   1.0000
  10 Distance restraints 2 (N-O)           :   1.0000
  11 Mainchain Phi dihedral restraints     :   1.0000
  12 Mainchain Psi dihedral restraints     :   1.0000
  13 Mainchain Omega dihedral restraints   :   1.0000
  14 Sidechain Chi_1 dihedral restraints   :   1.0000
  15 Sidechain Chi_2 dihedral restraints   :   1.0000
  16 Sidechain Chi_3 dihedral restraints   :   1.0000
  17 Sidechain Chi_4 dihedral restraints   :   1.0000
  18 Disulfide distance restraints         :   1.0000
  19 Disulfide angle restraints            :   1.0000
  20 Disulfide dihedral angle restraints   :   1.0000
  21 Lower bound distance restraints       :   1.0000
  22 Upper bound distance restraints       :   1.0000
  23 Distance restraints 3 (SDCH-MNCH)     :   1.0000
  24 Sidechain Chi_5 dihedral restraints   :   1.0000
  25 Phi/Psi pair of dihedral restraints   :   1.0000
  26 Distance restraints 4 (SDCH-SDCH)     :   1.0000
  27 Distance restraints 5 (X-Y)           :   1.0000
  28 NMR distance restraints 6 (X-Y)       :   1.0000
  29 NMR distance restraints 7 (X-Y)       :   1.0000
  30 Minimal distance restraints           :   1.0000
  31 Non-bonded restraints                 :   1.0000
  32 Atomic accessibility restraints       :   1.0000
  33 Atomic density restraints             :   1.0000

Results:
   Initial value of -Ln(Molecular pdf)     :    110257.03906
   Final value of -Ln(Molecular pdf)       :         0.20429
   Optimizer exit status                   :        0
   Numb of conjugate gradients cycles      :       53
   Numb of calls to Molecular pdf function :      107
   Numb of updates of dynamic contacts     :        0
   Numb of non-updates of dynamic contacts :      108
   Final max atom shift                    :   0.0084





>> ENERGY; Differences between the model's features and restraints:
chkcsp__W> no fixed restraints selected,
           there may be some dynamic ones.
chkcsp__W> you probably did not read the csrs file!
chkcmb__W> none of the needed non-bonded terms selected


ID1, ID2                                          :       1      1
Number of static restraints [all, selected]       :       0      0
Numb of non-bonded pairs                          :       0
Distance cutoff for non-bonded pairs search [A]   :        4.00000
Residue span range                                :       0  99999
Value of -Ln(Molecular pdf)                       :    0.20429    
Value of the symmetry term within -Ln(Mpdf)       :    0.20429    
Standard deviation for sphere overla (SPHERE_STDV):        0.05000
Radii factor (RADII_FACTOR)                       :        0.82000



Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   NUMVP   ... number of restraints with violation of PDF value > VIOL_REPORT_CUT2[i].
   RMS_1   ... rms(feature,minimally violated basis restraint,NUMB).
   RMS_2   ... rms(feature,ideal value,NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :       0       0      0   0.000   0.000    0.000000       1.000
 2 Bond angle potential               :       0       0      0   0.000   0.000    0.000000       1.000
 3 Stereochemical cosine torsion poten:       0       0      0   0.000   0.000    0.000000       1.000
 4 Stereochemical improper torsion pot:       0       0      0   0.000   0.000    0.000000       1.000
 5 soft-sphere overlap restraints     :       0       0      0   0.000   0.000    0.000000       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000    0.000000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000    0.000000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000    0.000000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000    0.000000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000    0.000000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000    0.000000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000    0.000000       1.000
13 Mainchain Omega dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
14 Sidechain Chi_1 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
15 Sidechain Chi_2 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
16 Sidechain Chi_3 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
17 Sidechain Chi_4 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000    0.000000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000    0.000000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000    0.000000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000    0.000000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000    0.000000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000    0.000000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000    0.000000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000    0.000000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000    0.000000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000    0.000000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000    0.000000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000    0.000000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000    0.000000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000    0.000000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the ideal value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers and names of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the ideal value (global minimum).
   VIOL   ... difference from the ideal value.
   RVIOL  ... relative difference from the ideal value.


<< end of ENERGY.


Report on the conjugate gradients optimization: 


Structure optimized:
   numb of all residues         :       24
   numb of all real atoms       :      100
   numb of selected real atoms  :      100
   numb of all pseudo atoms     :        0
   numb of selected pseudo atoms:        0

Restraints used:
   numb of static restraints         :      344
   numb of selected static restraints:      344
   numb of non-bonded pairs          :      187

Dynamic pairs routine 2: NATMxNATM cell sorting.

Parameters used:
   type of the optimization method                :        1
   RESIDUE_SPAN_RANGE                             :        0   99999
   RESIDUE_SPAN_SIGN                              :        T
   min atm shift before contacts update           :     0.39
   max atm shift that signals convergence         :   0.0100
   max allowed number of iterations               :      300
   restr res span triggering NlogN contacts alg   :       15
   cell size for dynamic pairs search [A]         :   4.0000

Scaling parameters:
   schedule                                :        1
   vdW contacts stand dev                  :   0.0500
   1 Bond length potential                 :   1.0000
   2 Bond angle potential                  :   1.0000
   3 Stereochemical cosine torsion potenti :   1.0000
   4 Stereochemical improper torsion poten :   1.0000
   5 soft-sphere overlap restraints        :   1.0000
   6 Lennard-Jones 6-12 potential          :   1.0000
   7 Coulomb point-point electrostatic pot :   1.0000
   8 H-bonding potential                   :   1.0000
   9 Distance restraints 1 (CA-CA)         :   1.0000
  10 Distance restraints 2 (N-O)           :   1.0000
  11 Mainchain Phi dihedral restraints     :   1.0000
  12 Mainchain Psi dihedral restraints     :   1.0000
  13 Mainchain Omega dihedral restraints   :   1.0000
  14 Sidechain Chi_1 dihedral restraints   :   1.0000
  15 Sidechain Chi_2 dihedral restraints   :   1.0000
  16 Sidechain Chi_3 dihedral restraints   :   1.0000
  17 Sidechain Chi_4 dihedral restraints   :   1.0000
  18 Disulfide distance restraints         :   1.0000
  19 Disulfide angle restraints            :   1.0000
  20 Disulfide dihedral angle restraints   :   1.0000
  21 Lower bound distance restraints       :   1.0000
  22 Upper bound distance restraints       :   1.0000
  23 Distance restraints 3 (SDCH-MNCH)     :   1.0000
  24 Sidechain Chi_5 dihedral restraints   :   1.0000
  25 Phi/Psi pair of dihedral restraints   :   1.0000
  26 Distance restraints 4 (SDCH-SDCH)     :   1.0000
  27 Distance restraints 5 (X-Y)           :   1.0000
  28 NMR distance restraints 6 (X-Y)       :   1.0000
  29 NMR distance restraints 7 (X-Y)       :   1.0000
  30 Minimal distance restraints           :   1.0000
  31 Non-bonded restraints                 :   1.0000
  32 Atomic accessibility restraints       :   1.0000
  33 Atomic density restraints             :   1.0000

Results:
   Initial value of -Ln(Molecular pdf)     :    661788.12500
   Final value of -Ln(Molecular pdf)       :        48.72377
   Optimizer exit status                   :        1
   Numb of conjugate gradients cycles      :      148
   Numb of calls to Molecular pdf function :      301
   Numb of updates of dynamic contacts     :       38
   Numb of non-updates of dynamic contacts :      264
   Final max atom shift                    :   0.0543





Report on the molecular dynamics optimization: 


Structure optimized:
   numb of all residues         :       24
   numb of all real atoms       :      100
   numb of selected real atoms  :      100
   numb of all pseudo atoms     :        0
   numb of selected pseudo atoms:        0

Restraints used:
   numb of static restraints         :      344
   numb of selected static restraints:      344
   numb of non-bonded pairs          :       32

Dynamic pairs routine 2: NATMxNATM cell sorting.

Parameters used:
   type of the optimization method                :        3
   temperature                                    :   293.00
   seed for the random number generator           :        1
   RESIDUE_SPAN_RANGE                             :        0   99999
   RESIDUE_SPAN_SIGN                              :        T
   min atm shift before contacts update           :     0.39
   max atm shift that signals convergence         :   0.0100
   molecular dynamics time step                   :   4.0000
   max allowed number of MD steps                 :      300
   restr res span triggering NlogN contacts alg   :       15
   cell size for dynamic pairs search [A]         :   4.0000

Scaling parameters:
   schedule                                :        1
   vdW contacts stand dev                  :   0.0500
   1 Bond length potential                 :   1.0000
   2 Bond angle potential                  :   1.0000
   3 Stereochemical cosine torsion potenti :   1.0000
   4 Stereochemical improper torsion poten :   1.0000
   5 soft-sphere overlap restraints        :   1.0000
   6 Lennard-Jones 6-12 potential          :   1.0000
   7 Coulomb point-point electrostatic pot :   1.0000
   8 H-bonding potential                   :   1.0000
   9 Distance restraints 1 (CA-CA)         :   1.0000
  10 Distance restraints 2 (N-O)           :   1.0000
  11 Mainchain Phi dihedral restraints     :   1.0000
  12 Mainchain Psi dihedral restraints     :   1.0000
  13 Mainchain Omega dihedral restraints   :   1.0000
  14 Sidechain Chi_1 dihedral restraints   :   1.0000
  15 Sidechain Chi_2 dihedral restraints   :   1.0000
  16 Sidechain Chi_3 dihedral restraints   :   1.0000
  17 Sidechain Chi_4 dihedral restraints   :   1.0000
  18 Disulfide distance restraints         :   1.0000
  19 Disulfide angle restraints            :   1.0000
  20 Disulfide dihedral angle restraints   :   1.0000
  21 Lower bound distance restraints       :   1.0000
  22 Upper bound distance restraints       :   1.0000
  23 Distance restraints 3 (SDCH-MNCH)     :   1.0000
  24 Sidechain Chi_5 dihedral restraints   :   1.0000
  25 Phi/Psi pair of dihedral restraints   :   1.0000
  26 Distance restraints 4 (SDCH-SDCH)     :   1.0000
  27 Distance restraints 5 (X-Y)           :   1.0000
  28 NMR distance restraints 6 (X-Y)       :   1.0000
  29 NMR distance restraints 7 (X-Y)       :   1.0000
  30 Minimal distance restraints           :   1.0000
  31 Non-bonded restraints                 :   1.0000
  32 Atomic accessibility restraints       :   1.0000
  33 Atomic density restraints             :   1.0000

Results:
   Initial value of -Ln(Molecular pdf)     :        48.72377
   Final value of -Ln(Molecular pdf)       :        72.55017
   Numb of iterations                      :      300
   Numb of updates of dynamic contacts     :       43
   Numb of non-updates of dynamic contacts :      258
   Final max atom shift                    :   0.0628
   Maximal energy, step                    :       106.46596      12
   Minimal energy, step                    :        48.72377       0
   Average energy, stand.dev.              :        81.33561        9.97959
   Average atomic shift along one axis     :         0.02663
   MODEL returned                          : FINAL





Report on the conjugate gradients optimization: 


Structure optimized:
   numb of all residues         :       24
   numb of all real atoms       :      100
   numb of selected real atoms  :      100
   numb of all pseudo atoms     :        0
   numb of selected pseudo atoms:        0

Restraints used:
   numb of static restraints         :      344
   numb of selected static restraints:      344
   numb of non-bonded pairs          :       34

Dynamic pairs routine 2: NATMxNATM cell sorting.

Parameters used:
   type of the optimization method                :        1
   RESIDUE_SPAN_RANGE                             :        0   99999
   RESIDUE_SPAN_SIGN                              :        T
   min atm shift before contacts update           :     0.39
   max atm shift that signals convergence         :   0.0100
   max allowed number of iterations               :      300
   restr res span triggering NlogN contacts alg   :       15
   cell size for dynamic pairs search [A]         :   4.0000

Scaling parameters:
   schedule                                :        1
   vdW contacts stand dev                  :   0.0500
   1 Bond length potential                 :   1.0000
   2 Bond angle potential                  :   1.0000
   3 Stereochemical cosine torsion potenti :   1.0000
   4 Stereochemical improper torsion poten :   1.0000
   5 soft-sphere overlap restraints        :   1.0000
   6 Lennard-Jones 6-12 potential          :   1.0000
   7 Coulomb point-point electrostatic pot :   1.0000
   8 H-bonding potential                   :   1.0000
   9 Distance restraints 1 (CA-CA)         :   1.0000
  10 Distance restraints 2 (N-O)           :   1.0000
  11 Mainchain Phi dihedral restraints     :   1.0000
  12 Mainchain Psi dihedral restraints     :   1.0000
  13 Mainchain Omega dihedral restraints   :   1.0000
  14 Sidechain Chi_1 dihedral restraints   :   1.0000
  15 Sidechain Chi_2 dihedral restraints   :   1.0000
  16 Sidechain Chi_3 dihedral restraints   :   1.0000
  17 Sidechain Chi_4 dihedral restraints   :   1.0000
  18 Disulfide distance restraints         :   1.0000
  19 Disulfide angle restraints            :   1.0000
  20 Disulfide dihedral angle restraints   :   1.0000
  21 Lower bound distance restraints       :   1.0000
  22 Upper bound distance restraints       :   1.0000
  23 Distance restraints 3 (SDCH-MNCH)     :   1.0000
  24 Sidechain Chi_5 dihedral restraints   :   1.0000
  25 Phi/Psi pair of dihedral restraints   :   1.0000
  26 Distance restraints 4 (SDCH-SDCH)     :   1.0000
  27 Distance restraints 5 (X-Y)           :   1.0000
  28 NMR distance restraints 6 (X-Y)       :   1.0000
  29 NMR distance restraints 7 (X-Y)       :   1.0000
  30 Minimal distance restraints           :   1.0000
  31 Non-bonded restraints                 :   1.0000
  32 Atomic accessibility restraints       :   1.0000
  33 Atomic density restraints             :   1.0000

Results:
   Initial value of -Ln(Molecular pdf)     :        72.55017
   Final value of -Ln(Molecular pdf)       :        21.99064
   Optimizer exit status                   :        0
   Numb of conjugate gradients cycles      :       23
   Numb of calls to Molecular pdf function :       47
   Numb of updates of dynamic contacts     :        2
   Numb of non-updates of dynamic contacts :       46
   Final max atom shift                    :   0.0076





>> ENERGY; Differences between the model's features and restraints:


ID1, ID2                                          :       1      1
Number of static restraints [all, selected]       :     344    344
Numb of non-bonded pairs                          :      34
Distance cutoff for non-bonded pairs search [A]   :        4.00000
Residue span range                                :       0  99999
Value of -Ln(Molecular pdf)                       :     21.991    
Value of the symmetry term within -Ln(Mpdf)       :     4.2793    
Standard deviation for sphere overla (SPHERE_STDV):        0.05000
Radii factor (RADII_FACTOR)                       :        0.82000



Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   NUMVP   ... number of restraints with violation of PDF value > VIOL_REPORT_CUT2[i].
   RMS_1   ... rms(feature,minimally violated basis restraint,NUMB).
   RMS_2   ... rms(feature,ideal value,NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :      96       0      0   0.001   0.001   0.5965002E-01   1.000
 2 Bond angle potential               :     116       0      0   0.619   0.619   0.8843371       1.000
 3 Stereochemical cosine torsion poten:     108       0      0  74.448  74.448    16.71591       1.000
 4 Stereochemical improper torsion pot:      24       0      0   0.242   0.242   0.5140700E-01   1.000
 5 soft-sphere overlap restraints     :      34       0      0   0.000   0.000    0.000000       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000    0.000000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000    0.000000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000    0.000000       1.000
 9 Distance restraints 1 (CA-CA)      :       0       0      0   0.000   0.000    0.000000       1.000
10 Distance restraints 2 (N-O)        :       0       0      0   0.000   0.000    0.000000       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000    0.000000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000    0.000000       1.000
13 Mainchain Omega dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
14 Sidechain Chi_1 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
15 Sidechain Chi_2 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
16 Sidechain Chi_3 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
17 Sidechain Chi_4 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000    0.000000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000    0.000000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000    0.000000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000    0.000000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000    0.000000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :       0       0      0   0.000   0.000    0.000000       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
25 Phi/Psi pair of dihedral restraints:       0       0      0   0.000   0.000    0.000000       1.000
26 Distance restraints 4 (SDCH-SDCH)  :       0       0      0   0.000   0.000    0.000000       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000    0.000000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000    0.000000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000    0.000000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000    0.000000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000    0.000000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000    0.000000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000    0.000000       1.000



List of the violated restraints:
   A restraint is violated when the relative difference
   from the ideal value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers and names of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the ideal value (global minimum).
   VIOL   ... difference from the ideal value.
   RVIOL  ... relative difference from the ideal value.



report___> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0    2    2    0    4    1    3    0    2    1    0



<< end of ENERGY.
iatmcls_W> MODEL atom not classified: GLY:OT1        
iatmcls_W> MODEL atom not classified: GLY:OT2        


SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL):



Least-squares superposition: 

     PICKed MODEL atoms are used for superposition if
     they have equivalent atoms in MODEL2

     Superposition done               :         T
     Numb of residues in MODEL        :         6
     Numb of atoms/sel atoms in MODEL :        25       25
     Numb of residues in MODEL2       :         6
     Numb of atoms in MODEL2          :        25
     Equivalences refinement          :         F
     Numb of aligned equiv positions  :        25
     Numb of aligned equiv distances  :       300
     RMS before superposition         :    7.2297
     RMS after superposition          :    0.6289
     DRMS                             :    0.0263

     Distance cutoff                  :    3.5000
     Numb of equiv cutoff positions   :        25
     Numb of equiv cutoff distances   :       300
     Cutoff RMS after superposition   :    0.6289
     Cutoff DRMS                      :    0.0263



SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL):



Least-squares superposition: 

     PICKed MODEL atoms are used for superposition if
     they have equivalent atoms in MODEL2

     Superposition done               :         T
     Numb of residues in MODEL        :         6
     Numb of atoms/sel atoms in MODEL :        25       25
     Numb of residues in MODEL2       :         6
     Numb of atoms in MODEL2          :        25
     Equivalences refinement          :         F
     Numb of aligned equiv positions  :        25
     Numb of aligned equiv distances  :       300
     RMS before superposition         :   14.3836
     RMS after superposition          :    0.1457
     DRMS                             :    0.0165

     Distance cutoff                  :    3.5000
     Numb of equiv cutoff positions   :        25
     Numb of equiv cutoff distances   :       300
     Cutoff RMS after superposition   :    0.1457
     Cutoff DRMS                      :    0.0165



SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL):



Least-squares superposition: 

     PICKed MODEL atoms are used for superposition if
     they have equivalent atoms in MODEL2

     Superposition done               :         T
     Numb of residues in MODEL        :         6
     Numb of atoms/sel atoms in MODEL :        25       25
     Numb of residues in MODEL2       :         6
     Numb of atoms in MODEL2          :        25
     Equivalences refinement          :         F
     Numb of aligned equiv positions  :        25
     Numb of aligned equiv distances  :       300
     RMS before superposition         :   21.4746
     RMS after superposition          :    0.1613
     DRMS                             :    0.0249

     Distance cutoff                  :    3.5000
     Numb of equiv cutoff positions   :        25
     Numb of equiv cutoff distances   :       300
     Cutoff RMS after superposition   :    0.1613
     Cutoff DRMS                      :    0.0249


Global dynamic memory allocated:    4034.700 kbytes.
Starting time                  : 1998/09/16  14:34:15
Closing time                   : 1998/09/16  14:34:29
