
 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 12:54:44 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      2.953027717    
 Double-ended search iterations= 385 RMS= 0.1674 Dev= 1.18% S= 43.94 time= 5.77
 Following    2 images are candidates for TS:    4   10  
 Converged to TS (number of iterations):         86
 Converged to TS (number of iterations):         75
 DNEB run yielded 2 true transition state(s) time=  15.97

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1073 steps. Energy=    -382.5427530       time=       3.90
 Minus side of path:                     917 steps. Energy=    -390.4787888       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5427530  5.7127         -376.8300957  13.649         -390.4787888  37.662  26.046   7.917  18.316
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     910 steps. Energy=    -390.4787888       time=       2.86
 Minus side of path:                    1022 steps. Energy=    -395.3198837       time=       3.47

         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  11.061  13.109
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     7013.5    
 decide> The unconnected minima in the chain and their distances are:
     2       19.14     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 175 RMS= 1.5164 Dev= 0.41% S= 19.57 time= 1.24
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        151
 DNEB run yielded 1 true transition state(s) time=  12.98

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     958 steps. Energy=    -388.2292954       time=       2.88
 Minus side of path:                     990 steps. Energy=    -390.5224747       time=       3.61

         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   3.287  44.113
        *NEW* (Placed in 5)                                     Known (#2)
 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      3 steps with      1 missing connections, weight=     3015.0    
 decide> The unconnected minima in the chain and their distances are:
     5       14.45     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 5.1778 Dev= 1.35% S= 14.53 time= 0.78
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.55
 isnewts> transition state is the same as number        2 energy=     -389.5874437403
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     873 steps. Energy=    -390.4787888       time=       2.15
 Minus side of path:                    1007 steps. Energy=    -395.3583493       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4787888 0.89135         -389.5874437  5.7709         -395.3583493  18.165  14.108  11.438  12.677
        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      4 steps with      1 missing connections, weight=     4836.3    
 decide> The unconnected minima in the chain and their distances are:
     5       16.91     4 
 

 tryconnect> 175-iteration DNEB run for minima 4_S and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 175 RMS= 0.4562 Dev= 1.11% S= 17.23 time= 1.29
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  26.54
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     4869.7    
 decide> The unconnected minima in the chain and their distances are:
     5       16.95     6 
 

 tryconnect> 175-iteration DNEB run for minima 5_F and 6_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 175 RMS= 0.3085 Dev= 1.36% S= 17.24 time= 1.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        107
 DNEB run yielded 1 true transition state(s) time=   7.39
 isnewts> transition state is the same as number        3 energy=     -387.6733421055
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     921 steps. Energy=    -388.2292954       time=       2.69
 Minus side of path:                     984 steps. Energy=    -390.5224747       time=       3.35

         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   3.285  44.135
        Known (#5)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6030.1    
 decide> The unconnected minima in the chain and their distances are:
     5       14.45     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 805 RMS= 0.0287 Dev= 4.85% S= 17.16 time= 26.10
 Following    1 images are candidates for TS:   21  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.34

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1121 steps. Energy=    -395.3583493       time=       3.81
 Minus side of path:                     894 steps. Energy=    -388.2292954       time=       2.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3583493  7.1575         -388.2008844 0.28411E-01     -388.2292954  17.674  16.960   3.120  46.476
        Known (#6)                                              Known (#5)
 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  37.662  26.046   7.917  18.316
   4     -390.4787888 0.89135        -389.5874437  5.7709        -395.3583493  18.165  14.108  11.438  12.677
   6     -395.3583493  7.1575        -388.2008844 0.28411E-01    -388.2292954  17.674  16.960   3.120  46.476
   3     -388.2292954 0.55595        -387.6733421  2.8491        -390.5224747  17.556  16.599   3.287  44.113

 Number of TS in the path       =      4
 Number of cycles               =      6

 Elapsed time=                               145.48
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             45787 time=          62.55 %= 43.0
 OPTIM> # of energy+gradient+Hessian calls=       732 time=           3.83 %=  2.6
