
 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)@comp24.ch.
                 Created on  5/28/12 at 12:49:12 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=    -382.5427530     RMS force=    0.9973453174E-06
 OPTIM> Final energy  =    -390.5224747     RMS force=    0.9029583014E-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=     54597.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.94     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 385 RMS= 0.1102 Dev= 1.10% S= 45.62 time= 5.70
 Following    2 images are candidates for TS:    4   10  
 Converged to TS (number of iterations):         66
 Converged to TS (number of iterations):         75
 DNEB run yielded 2 true transition state(s) time=  14.18

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1066 steps. Energy=    -382.5427530       time=       3.04
 Minus side of path:                     918 steps. Energy=    -390.4787888       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5427530  5.7127         -376.8300957  13.649         -390.4787888  37.663  26.048   7.906  18.341
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     926 steps. Energy=    -388.2292954       time=       2.53
 Minus side of path:                     998 steps. Energy=    -390.5224747       time=       3.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2292954 0.55595         -387.6733421  2.8491         -390.5224747  17.556  16.599   3.288  44.104
        *NEW* (Placed in 4)                                     Known (#2)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3015.0    
 decide> The unconnected minima in the chain and their distances are:
     4       14.45     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 4_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0487 Dev= 0.52% S= 14.58 time= 0.80
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.05

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     866 steps. Energy=    -388.2292954       time=       1.96
 Minus side of path:                    1119 steps. Energy=    -395.3583493       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2292954 0.28411E-01     -388.2008844  7.1575         -395.3583493  17.674  16.960   3.121  46.464
        Known (#4)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     2805.4    
 decide> The unconnected minima in the chain and their distances are:
     5       14.10     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1068 Dev= 0.30% S= 14.68 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   5.78

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     911 steps. Energy=    -390.4787888       time=       3.01
 Minus side of path:                    1010 steps. Energy=    -395.3198837       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4787888 0.89135         -389.5874437  5.7324         -395.3198837  18.402  14.600  11.058  13.113
        Known (#3)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3.1725    
 decide> The unconnected minima in the chain and their distances are:
     5        1.47     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 3.3411 Dev= 8.59% S= 1.58 time= 0.21
 Following    1 images are candidates for TS:    1  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   5.57

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     873 steps. Energy=    -395.3583493       time=       2.69
 Minus side of path:                    1088 steps. Energy=    -395.3264081       time=       2.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3583493 0.31642         -395.0419304 0.28448         -395.3264081  19.894  17.579   3.613  40.130
        Known (#5)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     6.3450    
 decide> The unconnected minima in the chain and their distances are:
     5        1.47     6 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 6_S using 3 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 0.0107 Dev= 0.48% S= 1.47 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.36

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     835 steps. Energy=    -395.3583493       time=       1.86
 Minus side of path:                     873 steps. Energy=    -395.3198837       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3583493 0.62230E-01     -395.2961192 0.23765E-01     -395.3198837   1.472   1.469   3.037  47.743
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -382.5427530  5.7127        -376.8300957  13.649        -390.4787888  37.663  26.048   7.906  18.341
   4     -390.4787888 0.89135        -389.5874437  5.7324        -395.3198837  18.402  14.600  11.058  13.113
   6     -395.3198837 0.23765E-01    -395.2961192 0.62230E-01    -395.3583493   1.472   1.469   3.037  47.743
   3     -395.3583493  7.1575        -388.2008844 0.28411E-01    -388.2292954  17.674  16.960   3.121  46.464
   2     -388.2292954 0.55595        -387.6733421  2.8491        -390.5224747  17.556  16.599   3.288  44.104

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

 Elapsed time=                                74.05
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             23081 time=          31.88 %= 43.0
 OPTIM> # of energy+gradient+Hessian calls=       271 time=           1.34 %=  1.8
