
 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 13:13:24 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -380.0677513     RMS force=    0.9921181688E-06
 OPTIM> Final energy  =    -385.0052262     RMS force=    0.9812633651E-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=     40714.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.40     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 350 RMS= 0.3136 Dev= 1.45% S= 38.15 time= 4.84
 Following    2 images are candidates for TS:    1    4  
 Converged to TS (number of iterations):         28
 Converged to TS (number of iterations):         86
 DNEB run yielded 2 true transition state(s) time=  11.17

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     978 steps. Energy=    -380.0677513       time=       2.85
 Minus side of path:                    1772 steps. Energy=    -391.7571917       time=      10.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.0677513 0.91644E-02     -380.0585869  11.699         -391.7571917  41.280  40.716   2.763  52.481
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1320 steps. Energy=    -391.1766914       time=       5.69
 Minus side of path:                     950 steps. Energy=    -381.0004776       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1766914  10.249         -380.9276941 0.72784E-01     -381.0004776  35.749  35.171   2.446  59.272
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2974.4    
 decide> The unconnected minima in the chain and their distances are:
     2       14.38     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_S using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 1.1462 Dev= 1.21% S= 15.30 time= 0.85
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.91

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     992 steps. Energy=    -385.5492809       time=       2.67
 Minus side of path:                     971 steps. Energy=    -389.0531689       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5492809  1.2060         -384.3432929  4.7099         -389.0531689  15.481  14.664  13.425  10.801
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     2816.6    
 decide> The unconnected minima in the chain and their distances are:
     2       10.71     6     7       11.66     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0266 Dev= 0.02% S= 10.73 time= 0.45
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.56

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     929 steps. Energy=    -385.0052262       time=       2.33
 Minus side of path:                     998 steps. Energy=    -385.5492809       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0052262 0.21186E-01     -384.9840403 0.56524         -385.5492809  11.212  10.716   2.231  65.002
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 7_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 105 RMS= 0.2584 Dev= 0.41% S= 12.30 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   5.27

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     952 steps. Energy=    -392.3683405       time=       2.41
 Minus side of path:                    1008 steps. Energy=    -391.7748680       time=       2.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.3683405  2.7746         -389.5937803  2.1811         -391.7748680  13.594  12.666   2.715  53.399
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2427.2    
 decide> The unconnected minima in the chain and their distances are:
     6       13.44     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 6_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 140 RMS= 2.8163 Dev= 1.20% S= 14.45 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.72

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     981 steps. Energy=    -389.0841692       time=       2.54
 Minus side of path:                     974 steps. Energy=    -385.5749777       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.0841692  4.7070         -384.3771803  1.1978         -385.5749777  14.227  13.521  15.393   9.420
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     936.44    
 decide> The unconnected minima in the chain and their distances are:
     6        1.08    11    10        9.78     3 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 11_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0239 Dev= 0.09% S= 1.08 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.48

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     894 steps. Energy=    -385.5492809       time=       2.07
 Minus side of path:                     907 steps. Energy=    -385.5749777       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5492809 0.19627E-01     -385.5296537 0.45324E-01     -385.5749777   1.094   1.078  25.010   5.798
        Known (#6)                                              Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 10_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3651 Dev= 0.87% S= 10.25 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   6.76

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     963 steps. Energy=    -389.0841692       time=       2.48
 Minus side of path:                     847 steps. Energy=    -388.9351428       time=       1.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.0841692 0.16738         -388.9167867 0.18356E-01     -388.9351428   7.517   7.447   5.026  28.849
        Known (#10)                                             *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1445.0    
 decide> The unconnected minima in the chain and their distances are:
    12       11.31     3 
 

 tryconnect> 105-iteration DNEB run for minima 3_S and 12_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2708 Dev= 0.11% S= 11.94 time= 0.47
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.72

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     967 steps. Energy=    -392.3855307       time=       2.30
 Minus side of path:                    1162 steps. Energy=    -391.6303934       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.3855307  2.7707         -389.6148095  2.0156         -391.6303934  16.591  13.548   2.795  51.882
        *NEW* (Placed in 13)                                    *NEW* (Placed in 14)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 14 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1870.4    
 decide> The unconnected minima in the chain and their distances are:
    10        9.78     3 
 

 tryconnect> 770-iteration DNEB run for minima 3_S and 10_F using 22 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 770 RMS= 0.1449 Dev= 4.03% S= 14.59 time= 24.00
 Following    3 images are candidates for TS:    6   13   18  
 Converged to TS (number of iterations):         14
 Converged to TS (number of iterations):         18
 Converged to TS (number of iterations):         21
 DNEB run yielded 3 true transition state(s) time=   9.44
 isnewts> transition state is the same as number        9 energy=     -389.6148094884
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1173 steps. Energy=    -391.6303934       time=       3.26
 Minus side of path:                     935 steps. Energy=    -391.7571917       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.6303934  2.0059         -389.6244796  2.1327         -391.7571917  17.632  16.348   2.520  57.550
        Known (#14)                                             Known (#3)
 Unconnected minimum 14 found its way to S set.

 >>>>>  Path run for ts 11 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     978 steps. Energy=    -392.3855307       time=       2.34
 Minus side of path:                    1176 steps. Energy=    -391.6303934       time=       3.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.3855307  2.7707         -389.6148095  2.0156         -391.6303934  16.590  13.547   2.795  51.878
        Known (#13)                                             Known (#14)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     968 steps. Energy=    -389.0841692       time=       2.32
 Minus side of path:                     966 steps. Energy=    -392.3855307       time=       2.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.0841692  2.4093         -386.6749164  5.7106         -392.3855307  10.783   5.249   4.613  31.435
        Known (#10)                                             Known (#13)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -380.0677513 0.91644E-02    -380.0585869  11.699        -391.7571917  41.280  40.716   2.763  52.481
  10     -391.7571917  2.1327        -389.6244796  2.0059        -391.6303934  17.632  16.348   2.520  57.550
   9     -391.6303934  2.0156        -389.6148095  2.7707        -392.3855307  16.591  13.548   2.795  51.882
  12     -392.3855307  5.7106        -386.6749164  2.4093        -389.0841692  10.783   5.249   4.613  31.435
   6     -389.0841692  4.7070        -384.3771803  1.1978        -385.5749777  14.227  13.521  15.393   9.420
   7     -385.5749777 0.45324E-01    -385.5296537 0.19627E-01    -385.5492809   1.094   1.078  25.010   5.798
   4     -385.5492809 0.56524        -384.9840403 0.21186E-01    -385.0052262  11.212  10.716   2.231  65.002

 Number of TS in the path       =      7
 Number of cycles               =      7

 Elapsed time=                               157.63
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             59346 time=          80.89 %= 51.3
 OPTIM> # of energy+gradient+Hessian calls=       436 time=           1.81 %=  1.1
