
 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)@comp28.ch.
                 Created on  5/28/12 at 12:35: 2 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=    -385.3045545     RMS force=    0.9414349091E-06
 OPTIM> Final energy  =    -381.3109698     RMS force=    0.9901354532E-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=    0.19346E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.84     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 595 RMS= 0.0940 Dev= 4.65% S= 72.45 time= 12.03
 Following    2 images are candidates for TS:    7   13  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):        132
 DNEB run yielded 1 true transition state(s) time=  37.80

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1003 steps. Energy=    -377.5175935       time=       2.13
 Minus side of path:                    2096 steps. Energy=    -390.0195607       time=      13.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.5175935 0.12907E-01     -377.5046865  12.515         -390.0195607  60.310  58.903   1.615  89.807
        *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=    0.10740E+06
 decide> The unconnected minima in the chain and their distances are:
     2       45.59     3     3       23.31     1 
 

 tryconnect> 455-iteration DNEB run for minima 2_F and 3_U using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.1053 Dev= 2.85% S= 49.66 time= 6.94
 Following    1 images are candidates for TS:    7  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  19.43

 tryconnect> 210-iteration DNEB run for minima 1_S and 3_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1673 Dev= 0.62% S= 25.66 time= 1.44
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        104
 DNEB run yielded 1 true transition state(s) time=  14.83

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1118 steps. Energy=    -384.1502218       time=       3.30
 Minus side of path:                    1080 steps. Energy=    -382.3727169       time=       4.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1502218  4.6854         -379.4648063  2.9079         -382.3727169  40.005  38.094   2.885  50.257
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=    0.11911E+06
 decide> The unconnected minima in the chain and their distances are:
     2       44.39     6     6       31.62     1 
 

 tryconnect> 455-iteration DNEB run for minima 2_F and 6_U using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0522 Dev= 1.57% S= 54.17 time= 7.21
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        202
 DNEB run yielded 1 true transition state(s) time=  20.76

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1041 steps. Energy=    -377.5175935       time=       2.69
 Minus side of path:                    1194 steps. Energy=    -384.1502218       time=       4.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.5175935 0.33467         -377.1829240  6.9673         -384.1502218  48.436  39.142   1.790  81.026
        Known (#3)                                              Known (#5)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 6_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0509 Dev= 0.54% S= 33.31 time= 3.43
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.15

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     989 steps. Energy=    -382.3727169       time=       2.39
 Minus side of path:                    1130 steps. Energy=    -385.3045545       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.3727169  1.1132         -381.2594862  4.0451         -385.3045545  34.186  31.667   2.325  62.357
        Known (#6)                                              Known (#1)
 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      2 steps with      1 missing connections, weight=    0.17499E+06
 decide> The unconnected minima in the chain and their distances are:
     2       44.39     6 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 6_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2575150228    
 Double-ended search iterations= 805 RMS= 0.0352 Dev= 3.98% S= 59.14 time= 21.90
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        188
 DNEB run yielded 1 true transition state(s) time=  14.55
 isnewts> transition state is the same as number        3 energy=     -377.1829239578
 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:                    1194 steps. Energy=    -384.1502218       time=       4.05
 Minus side of path:                    1037 steps. Energy=    -377.5175935       time=       3.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1502218  6.9673         -377.1829240 0.33467         -377.5175935  48.431  39.130   1.789  81.032
        Known (#5)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.18947E+06
 decide> The unconnected minima in the chain and their distances are:
     2       45.59     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 805 RMS= 0.0420 Dev= 6.77% S= 53.70 time= 21.19
 Following    2 images are candidates for TS:   11   19  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  24.98
 isnewts> transition state is the same as number        1 energy=     -377.5046864678
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    2045 steps. Energy=    -390.0195607       time=      14.08
 Minus side of path:                     985 steps. Energy=    -377.5175935       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.0195607  12.515         -377.5046865 0.12907E-01     -377.5175935  60.299  58.892   1.616  89.703
        Known (#4)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=    0.27973E+06
 decide> The unconnected minima in the chain and their distances are:
     2       65.40     4 
 

 tryconnect> 665-iteration DNEB run for minima 2_F and 4_S using 19 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 665 RMS= 0.1349 Dev= 8.05% S= 81.82 time= 15.96
 Following    2 images are candidates for TS:    4   15  
 Converged to TS (number of iterations):         36
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time=  24.36

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1946 steps. Energy=    -390.0195607       time=      10.16
 Minus side of path:                    1018 steps. Energy=    -381.3109698       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.0195607  10.807         -379.2124765  2.0985         -381.3109698  69.456  65.602   1.942  74.677
        Known (#4)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -385.3045545  4.0451        -381.2594862  1.1132        -382.3727169  34.186  31.667   2.325  62.357
   2     -382.3727169  2.9079        -379.4648063  4.6854        -384.1502218  40.005  38.094   2.885  50.257
   3     -384.1502218  6.9673        -377.1829240 0.33467        -377.5175935  48.436  39.142   1.790  81.026
   1     -377.5175935 0.12907E-01    -377.5046865  12.515        -390.0195607  60.310  58.903   1.615  89.807
   7     -390.0195607  10.807        -379.2124765  2.0985        -381.3109698  69.456  65.602   1.942  74.677

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               323.97
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            109979 time=         125.83 %= 38.8
 OPTIM> # of energy+gradient+Hessian calls=      1732 time=           8.25 %=  2.5
