
 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)@comp27.ch.
                 Created on  5/28/12 at 12:54:51 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=    -388.3575902     RMS force=    0.9042067956E-06
 OPTIM> Final energy  =    -383.0206471     RMS force=    0.9368276356E-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=     46586.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.98     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 350 RMS= 0.5574 Dev= 2.72% S= 42.72 time= 4.21
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   6.45

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1349 steps. Energy=    -380.3476922       time=       5.57
 Minus side of path:                    1167 steps. Energy=    -385.7707842       time=       5.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.3476922  2.9525         -377.3951850  8.3756         -385.7707842  53.128  48.318   2.226  65.140
        *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      3 steps with      2 missing connections, weight=     48441.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.82     3     4       25.32     1 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 3_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 315 RMS= 0.1545 Dev= 1.41% S= 33.78 time= 3.39
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   8.07

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    2747 steps. Energy=    -391.6476196       time=      24.28
 Minus side of path:                    1024 steps. Energy=    -380.0521365       time=       4.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.6476196  11.904         -379.7434802 0.30866         -380.0521365  55.414  52.541   2.643  54.868
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      60.81406943    
 Double-ended search iterations= 245 RMS= 1.6552 Dev= 1.71% S= 27.71 time= 2.22
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   8.17

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     985 steps. Energy=    -385.7707842       time=       2.46
 Minus side of path:                     977 steps. Energy=    -385.7707842       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7707842  6.4704         -379.3004181  6.4704         -385.7707842   9.042   3.058  72.355   2.004
        Known (#4)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     54985.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.60     6     6       21.08     3     4       25.32     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 6_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 245 RMS= 0.3495 Dev= 1.02% S= 24.80 time= 2.01
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   4.90

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1001 steps. Energy=    -383.0471519       time=       2.20
 Minus side of path:                    2691 steps. Energy=    -394.4983358       time=      16.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0471519  2.6347         -380.4124077  14.086         -394.4983358  72.048  64.925   2.541  57.075
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 3_U and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 210 RMS= 0.0879 Dev= 1.16% S= 21.71 time= 1.46
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   6.74

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1082 steps. Energy=    -380.3476922       time=       2.50
 Minus side of path:                    1085 steps. Energy=    -380.0521365       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.3476922 0.82030         -379.5273891 0.52475         -380.0521365  25.737  21.117   6.721  21.574
        Known (#3)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 805 RMS= 0.2133 Dev= 1.59% S= 35.67 time= 23.45
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):        158
 DNEB run yielded 1 true transition state(s) time=  12.88

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     983 steps. Energy=    -384.9060936       time=       2.21
 Minus side of path:                     967 steps. Energy=    -380.7388602       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.9060936  4.6323         -380.2737939 0.46507         -380.7388602  12.971  12.684   2.685  54.006
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      4 missing connections, weight=     34335.    
 decide> The unconnected minima in the chain and their distances are:
     2        0.87     7     8       17.70     5     4       17.43     9    10       28.64     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0287 Dev= 0.19% S= 0.88 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.71

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     967 steps. Energy=    -383.0206471       time=       2.11
 Minus side of path:                     962 steps. Energy=    -383.0471519       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0206471 0.22140E-01     -382.9985073 0.48645E-01     -383.0471519   0.884   0.873  30.759   4.714
        Known (#2)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 5_U and 8_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      33.86354941    
 Double-ended search iterations= 175 RMS= 3.7127 Dev= 2.87% S= 17.77 time= 1.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   5.66

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     976 steps. Energy=    -394.9440751       time=       2.45
 Minus side of path:                     965 steps. Energy=    -391.6476196       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.9440751  3.3248         -391.6192506 0.28369E-01     -391.6476196  10.832  10.392   3.223  44.988
        *NEW* (Placed in 11)                                    Known (#5)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 4_U and 9_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 300 RMS= 14.8492 Dev= 58.68% S= 19.99 time= 1.93
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   4.83

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     946 steps. Energy=    -384.9060936       time=       2.06
 Minus side of path:                     998 steps. Energy=    -385.7707842       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.9060936 0.52442         -384.3816714  1.3891         -385.7707842  18.417  17.435   4.776  30.360
        Known (#9)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 10_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      57.91816136    
 Double-ended search iterations= 280 RMS= 1.4712 Dev= 1.26% S= 30.99 time= 2.74
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=   6.21
 isnewts> transition state is the same as number        6 energy=     -380.2737938671
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     991 steps. Energy=    -380.7388602       time=       2.33
 Minus side of path:                     986 steps. Energy=    -384.9060936       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7388602 0.46507         -380.2737939  4.6323         -384.9060936  12.971  12.684   2.689  53.926
        Known (#10)                                             Known (#9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     25150.    
 decide> The unconnected minima in the chain and their distances are:
     8       11.28    11     9       28.73     1 
 

 tryconnect> 105-iteration DNEB run for minima 8_F and 11_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      22.92018318    
 Double-ended search iterations= 105 RMS= 0.2954 Dev= 3.74% S= 11.30 time= 0.43
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.10

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     819 steps. Energy=    -394.4983358       time=       2.01
 Minus side of path:                     955 steps. Energy=    -394.9440751       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.4983358 0.33364E-02     -394.4949995 0.44908         -394.9440751  11.381  11.282   4.389  33.036
        Known (#8)                                              Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 9_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      21.82874588    
 Double-ended search iterations= 280 RMS= 0.6140 Dev= 1.08% S= 31.59 time= 2.82
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        156
 DNEB run yielded 1 true transition state(s) time=  12.99
 isnewts> transition state is the same as number        6 energy=     -380.2737938671
 tryconnect> Will not repeat search for TS      1 same as TS      6
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     45484.    
 decide> The unconnected minima in the chain and their distances are:
     7       35.70     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 7_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 350 RMS= 0.5961 Dev= 1.91% S= 50.04 time= 4.25
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):         95
 Converged to TS (number of iterations):         41
 DNEB run yielded 2 true transition state(s) time=  11.74

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1050 steps. Energy=    -384.1502218       time=       2.72
 Minus side of path:                    1066 steps. Energy=    -388.3575902       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1502218  2.4106         -381.7395942  6.6180         -388.3575902  48.178  39.245   3.925  36.940
        *NEW* (Placed in 12)                                    Known (#1)
 Unconnected minimum 12 found its way to S set.

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                    1044 steps. Energy=    -384.1502218       time=       2.79
 Minus side of path:                    1020 steps. Energy=    -383.0206471       time=       2.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1502218  4.4727         -379.6775295  3.3431         -383.0206471  22.224  10.636  17.199   8.431
        Known (#12)                                             Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  12     -388.3575902  6.6180        -381.7395942  2.4106        -384.1502218  48.178  39.245   3.925  36.940
  13     -384.1502218  4.4727        -379.6775295  3.3431        -383.0206471  22.224  10.636  17.199   8.431

 Number of TS in the path       =      2
 Number of cycles               =      6

 Elapsed time=                               251.72
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             85341 time=         102.43 %= 40.7
 OPTIM> # of energy+gradient+Hessian calls=      1022 time=           4.36 %=  1.7
