
 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)@comp31.ch.
                 Created on  5/28/12 at 13: 1:47 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=    -377.4835589     RMS force=    0.9542750549E-06
 OPTIM> Final energy  =    -384.2210684     RMS force=    0.8620414912E-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=     12188.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.01     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 210 RMS= 0.4696 Dev= 0.84% S= 27.23 time= 1.40
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   7.11

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1003 steps. Energy=    -377.4835589       time=       3.62
 Minus side of path:                    1235 steps. Energy=    -382.0032988       time=       4.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.4835589 0.78558         -376.6979758  5.3053         -382.0032988  24.094  19.092   2.475  58.581
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3029.3    
 decide> The unconnected minima in the chain and their distances are:
     2       14.47     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 0.7178 Dev= 1.08% S= 20.32 time= 0.62
 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=  20.13
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6058.6    
 decide> The unconnected minima in the chain and their distances are:
     2       14.47     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 805 RMS= 0.1665 Dev= 4.83% S= 27.50 time= 20.45
 Following    1 images are candidates for TS:   14  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.83
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     24375.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.01     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 805 RMS= 3.8531 Dev= 5.37% S= 38.02 time= 20.34
 Following    4 images are candidates for TS:    1    6   10   14  
 Converged to TS (number of iterations):         26
 Converged to TS (number of iterations):         85
 Converged to TS (number of iterations):         73
 Converged to TS (number of iterations):        179
 DNEB run yielded 4 true transition state(s) time=  35.02
 isnewts> transition state is the same as number        1 energy=     -376.6979757963
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1019 steps. Energy=    -377.4835589       time=       3.19
 Minus side of path:                    1262 steps. Energy=    -382.0032988       time=       5.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.4835589 0.78558         -376.6979758  5.3053         -382.0032988  24.085  19.072   2.484  58.382
        Known (#1)                                              Known (#3)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1007 steps. Energy=    -382.0032988       time=       4.42
 Minus side of path:                    1778 steps. Energy=    -387.0976307       time=       8.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0032988 0.18422         -381.8190777  5.2786         -387.0976307  55.617  52.988   1.731  83.751
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1339 steps. Energy=    -382.0032988       time=       4.07
 Minus side of path:                    1571 steps. Energy=    -383.1435123       time=       5.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0032988  5.9605         -376.0428171  7.1007         -383.1435123  54.451  11.932  11.681  12.413
        Known (#3)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1002 steps. Energy=    -386.0632714       time=       2.57
 Minus side of path:                    1017 steps. Energy=    -384.2210684       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0632714  2.4605         -383.6027342 0.61833         -384.2210684  25.531  25.117   2.454  59.091
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2477.6    
 decide> The unconnected minima in the chain and their distances are:
     2       13.53     5 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 5_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2119 Dev= 0.41% S= 14.04 time= 0.62
 Following    1 images are candidates for TS:    3  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.46
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4955.2    
 decide> The unconnected minima in the chain and their distances are:
     2       13.53     5 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 5_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 805 RMS= 0.0084 Dev= 4.95% S= 16.16 time= 19.98
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.73

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1031 steps. Energy=    -384.2210684       time=       2.43
 Minus side of path:                    1013 steps. Energy=    -383.1435123       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2210684  7.6551         -376.5659936  6.5775         -383.1435123  20.627  13.559   1.918  75.609
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -377.4835589 0.78558        -376.6979758  5.3053        -382.0032988  24.094  19.092   2.475  58.581
   4     -382.0032988  5.9605        -376.0428171  7.1007        -383.1435123  54.451  11.932  11.681  12.413
   6     -383.1435123  6.5775        -376.5659936  7.6551        -384.2210684  20.627  13.559   1.918  75.609

 Number of TS in the path       =      3
 Number of cycles               =      6

 Elapsed time=                               222.11
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             85295 time=          89.94 %= 40.5
 OPTIM> # of energy+gradient+Hessian calls=      1206 time=           5.21 %=  2.3
