
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> Number of atoms (or variables)  determined as    145
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     6
CHARMMTYPE set to  2
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 35b4   February 15, 2010   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.16.54-0.2.5-smp(x86_64)@comp32.ch.
                 Created on  5/28/12 at 13: 2:12 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> * INPUT FILE FOR TRYPZIP 1LE1
 RDTITL> *
  
 CHARMM>    BOMLev -2
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 1
 NBOND          152
 NTHETA          223
 NPHI           88

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           24
 chsetdihe> NOMEGAC           11
 chsetdihe> NSIDECHAIN           27
 chsetdihe> NCHIRAL           13

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            24
 chsetdihe> NOMEGACTOT=            11
 chsetdihe> NSIDECHAINTOT=            27
 chsetdihe> NCHIRALTOT=            13

 chsetdihe>            51  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1     145

 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  435 Cartesian coordinates will be optimised for  145 CHARMM atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -385.8079668     RMS force=    0.9722541170E-06
 OPTIM> Final energy  =    -385.2626841     RMS force=    0.9578389499E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1067.2    
 decide> The unconnected minima in the chain and their distances are:
     2       10.22     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 105 RMS= 1.0785 Dev= 0.95% S= 15.01 time= 0.34
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   6.03

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     993 steps. Energy=    -385.2626841       time=       3.04
 Minus side of path:                    1973 steps. Energy=    -383.9142203       time=      12.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2626841  6.8018         -378.4609317  5.4533         -383.9142203  65.819  59.047   1.792  80.930
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2134.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.22     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 805 RMS= 0.1201 Dev= 4.32% S= 21.31 time= 20.12
 Following    3 images are candidates for TS:    2   11   17  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         73
 Converged to TS (number of iterations):         28
 DNEB run yielded 3 true transition state(s) time=  14.05

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1000 steps. Energy=    -385.8079668       time=       2.63
 Minus side of path:                     998 steps. Energy=    -386.8129981       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8079668  2.5002         -383.3077684  3.5052         -386.8129981   5.606   5.415   7.424  19.531
        Known (#1)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1095 steps. Energy=    -383.7749650       time=       3.53
 Minus side of path:                    1207 steps. Energy=    -381.1556837       time=       4.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7749650  3.3590         -380.4160082 0.73968         -381.1556837  37.210  31.954   2.006  72.295
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1010 steps. Energy=    -379.6292852       time=       3.58
 Minus side of path:                    1005 steps. Energy=    -381.5270744       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6292852 0.94401         -378.6852711  2.8418         -381.5270744   6.590   6.170  27.820   5.212
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     529.10    
 decide> The unconnected minima in the chain and their distances are:
     2        8.09     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 4.7890 Dev= 2.20% S= 8.79 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.48

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1010 steps. Energy=    -387.1186528       time=       2.45
 Minus side of path:                    1011 steps. Energy=    -385.2626841       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1186528  4.8706         -382.2480505  3.0146         -385.2626841  12.088   4.668   3.230  44.895
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1029.5    
 decide> The unconnected minima in the chain and their distances are:
     9       10.10     4 
 

 tryconnect> 105-iteration DNEB run for minima 4_S and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 105 RMS= 0.1897 Dev= 0.60% S= 10.57 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     975 steps. Energy=    -387.8018809       time=       2.10
 Minus side of path:                     979 steps. Energy=    -386.8129981       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8018809  1.0589         -386.7430140 0.69984E-01     -386.8129981  10.124   9.541   1.679  86.370
        *NEW* (Placed in 10)                                    Known (#4)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     128.13    
 decide> The unconnected minima in the chain and their distances are:
     9        5.04    10 
 

 tryconnect> 70-iteration DNEB run for minima 9_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4803 Dev= 3.07% S= 5.37 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.59

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1026 steps. Energy=    -387.1186528       time=       3.27
 Minus side of path:                     998 steps. Energy=    -386.2874961       time=       3.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1186528 0.96050         -386.1581563 0.12934         -386.2874961   6.020   5.807   2.047  70.845
        Known (#9)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     125.77    
 decide> The unconnected minima in the chain and their distances are:
    11        5.01    10 
 

 tryconnect> 70-iteration DNEB run for minima 10_S and 11_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.2278 Dev= 1.42% S= 5.33 time= 0.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.57

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1013 steps. Energy=    -386.2874961       time=       2.30
 Minus side of path:                     997 steps. Energy=    -387.8018809       time=       2.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2874961  2.4159         -383.8715811  3.9303         -387.8018809   6.316   5.011  22.748   6.374
        Known (#11)                                             Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -385.8079668  2.5002        -383.3077684  3.5052        -386.8129981   5.606   5.415   7.424  19.531
   6     -386.8129981 0.69984E-01    -386.7430140  1.0589        -387.8018809  10.124   9.541   1.679  86.370
   8     -387.8018809  3.9303        -383.8715811  2.4159        -386.2874961   6.316   5.011  22.748   6.374
   7     -386.2874961 0.12934        -386.1581563 0.96050        -387.1186528   6.020   5.807   2.047  70.845
   5     -387.1186528  4.8706        -382.2480505  3.0146        -385.2626841  12.088   4.668   3.230  44.895

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               115.84
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             45341 time=          47.86 %= 41.3
 OPTIM> # of energy+gradient+Hessian calls=       301 time=           1.16 %=  1.0
