
 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 12:47:10 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=    -376.9408748     RMS force=    0.8608006249E-06
 OPTIM> Final energy  =    -385.5525383     RMS force=    0.8632545197E-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=     30174.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.13     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      37.33456322    
 Double-ended search iterations= 315 RMS= 0.6633 Dev= 0.13% S= 31.68 time= 3.73
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        231
 DNEB run yielded 1 true transition state(s) time=  22.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1393 steps. Energy=    -387.1249825       time=       7.41
 Minus side of path:                    1026 steps. Energy=    -384.5228273       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1249825  5.0481         -382.0769039  2.4459         -384.5228273  28.097  14.122   6.874  21.093
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     27188.    
 decide> The unconnected minima in the chain and their distances are:
     2       12.75     4     4       29.29     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 7.9758 Dev= 8.70% S= 34.32 time= 0.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   4.70

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     926 steps. Energy=    -385.5525383       time=       2.98
 Minus side of path:                    1147 steps. Energy=    -384.5228273       time=       4.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5525383  3.0241         -382.5284662  1.9944         -384.5228273  20.820  12.752   4.066  35.659
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 4_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      63.85477290    
 Double-ended search iterations= 280 RMS= 0.7495 Dev= 0.67% S= 29.75 time= 2.99
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        181
 DNEB run yielded 1 true transition state(s) time=  14.84

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     983 steps. Energy=    -383.3252074       time=       2.44
 Minus side of path:                    1031 steps. Energy=    -387.4558761       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.3252074 0.34354         -382.9816663  4.4742         -387.4558761  23.964  21.951   2.302  62.981
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     26342.    
 decide> The unconnected minima in the chain and their distances are:
     3       29.75     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 280 RMS= 0.3192 Dev= 0.49% S= 30.88 time= 3.01
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        140
 DNEB run yielded 1 true transition state(s) time=  11.92
 isnewts> transition state is the same as number        1 energy=     -382.0769039080
 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:                     991 steps. Energy=    -382.5422012       time=       3.32
 Minus side of path:                    1032 steps. Energy=    -384.5228273       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5422012 0.46530         -382.0769039  2.4459         -384.5228273  18.609  14.486   6.488  22.351
        *NEW* (Placed in 7)                                     Known (#4)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     18620.    
 decide> The unconnected minima in the chain and their distances are:
     7       26.51     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 7_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 245 RMS= 3.6243 Dev= 0.80% S= 26.90 time= 2.28
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        128
 DNEB run yielded 1 true transition state(s) time=  10.45

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     877 steps. Energy=    -381.6887503       time=       2.54
 Minus side of path:                    1135 steps. Energy=    -385.5525383       time=       4.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.6887503 0.25860E-03     -381.6884917  3.8640         -385.5525383  13.084  12.739   3.888  37.290
        *NEW* (Placed in 8)                                     Known (#2)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     24618.    
 decide> The unconnected minima in the chain and their distances are:
     8       29.09     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 8_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      21.82874588    
 Double-ended search iterations= 280 RMS= 0.3019 Dev= 0.24% S= 29.48 time= 3.04
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=  11.66

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1289 steps. Energy=    -385.5525383       time=       5.61
 Minus side of path:                    1032 steps. Energy=    -388.3048300       time=       3.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5525383  4.8132         -380.7393683  7.5655         -388.3048300  31.237  14.910   5.459  26.564
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     28064.    
 decide> The unconnected minima in the chain and their distances are:
     9       30.39     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 9_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      22.92018318    
 Double-ended search iterations= 315 RMS= 0.2434 Dev= 0.54% S= 31.21 time= 3.85
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  18.58
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     28768.    
 decide> The unconnected minima in the chain and their distances are:
     2       12.98     5     5       29.84     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 0.8378 Dev= 6.00% S= 13.01 time= 0.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   8.68

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     943 steps. Energy=    -383.3252074       time=       3.12
 Minus side of path:                     925 steps. Energy=    -383.2736217       time=       3.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.3252074 0.14096         -383.1842434 0.89378E-01     -383.2736217   8.175   8.032   3.389  42.789
        Known (#5)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 5_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      43.21942375    
 Double-ended search iterations= 280 RMS= 0.6675 Dev= 0.26% S= 30.43 time= 3.06
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        136
 DNEB run yielded 1 true transition state(s) time=   9.83

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     933 steps. Energy=    -383.2736217       time=       2.49
 Minus side of path:                     964 steps. Energy=    -385.5525383       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.2736217 0.13982         -383.1338061  2.4187         -385.5525383  10.825  10.329   2.501  57.984
        Known (#10)                                             Known (#2)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     37241.    
 decide> The unconnected minima in the chain and their distances are:
     7       26.51     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 7_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.0848 Dev= 4.16% S= 31.57 time= 24.55
 Following    2 images are candidates for TS:    1   13  
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):        105
 DNEB run yielded 2 true transition state(s) time=  13.88
 isnewts> transition state is the same as number        1 energy=     -382.0769039080
 tryconnect> Will not repeat search for TS      2 same as TS      1

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     918 steps. Energy=    -376.9408748       time=       2.96
 Minus side of path:                    1253 steps. Energy=    -381.4644486       time=       3.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.9408748 0.21807         -376.7228083  4.7416         -381.4644486  24.879  23.672   2.171  66.779
        Known (#1)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     2627.6    
 decide> The unconnected minima in the chain and their distances are:
     5       13.80    11 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 11_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      26.53297705    
 Double-ended search iterations= 140 RMS= 2.0229 Dev= 1.95% S= 18.27 time= 0.74
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   5.34

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1083 steps. Energy=    -385.5525383       time=       4.36
 Minus side of path:                    1015 steps. Energy=    -381.4644486       time=       4.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5525383  8.5988         -376.9537794  4.5107         -381.4644486  27.812  15.637   4.956  29.260
        Known (#2)                                              Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -376.9408748 0.21807        -376.7228083  4.7416        -381.4644486  24.879  23.672   2.171  66.779
  10     -381.4644486  4.5107        -376.9537794  8.5988        -385.5525383  27.812  15.637   4.956  29.260

 Number of TS in the path       =      2
 Number of cycles               =      9

 Elapsed time=                               253.57
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             71385 time=          93.68 %= 36.9
 OPTIM> # of energy+gradient+Hessian calls=      1493 time=           7.53 %=  3.0
