
 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)@comp25.ch.
                 Created on  5/28/12 at 12:38:33 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -389.2335056     RMS force=    0.9313438436E-06
 OPTIM> Final energy  =    -389.1046918     RMS force=    0.8739094660E-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=    0.12925E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.56     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 525 RMS= 0.1357 Dev= 7.01% S= 67.62 time= 11.01
 Following    2 images are candidates for TS:    8   11  
 Converged to TS (number of iterations):         92
 Converged to TS (number of iterations):         64
 DNEB run yielded 2 true transition state(s) time=  16.74

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1078 steps. Energy=    -388.2386015       time=       3.67
 Minus side of path:                    1113 steps. Energy=    -388.3871812       time=       4.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2386015  3.5947         -384.6439207  3.7433         -388.3871812  47.259  42.195   3.256  44.536
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     964 steps. Energy=    -385.4005012       time=       3.14
 Minus side of path:                     974 steps. Energy=    -388.6809028       time=       3.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4005012 0.50217         -384.8983285  3.7826         -388.6809028  20.588  19.380   2.513  57.693
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     29350.    
 decide> The unconnected minima in the chain and their distances are:
     2        7.82     5     6       26.25     3     4       22.10     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2439 Dev= 0.07% S= 7.95 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.63

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     932 steps. Energy=    -385.4120596       time=       2.46
 Minus side of path:                    1044 steps. Energy=    -390.5554047       time=       4.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4120596 0.47753         -384.9345330  5.6209         -390.5554047  13.458  11.904   7.849  18.473
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 3_U and 6_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0521 Dev= 0.32% S= 26.96 time= 2.57
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.97

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     884 steps. Energy=    -388.2386015       time=       2.61
 Minus side of path:                     995 steps. Energy=    -388.5796269       time=       3.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2386015 0.87707         -387.3615291  1.2181         -388.5796269  14.127  13.006   2.084  69.585
        Known (#3)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0667 Dev= 0.17% S= 22.50 time= 1.81
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.35

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     975 steps. Energy=    -388.3871812       time=       2.31
 Minus side of path:                     989 steps. Energy=    -389.1997633       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3871812 0.64887         -387.7383072  1.4615         -389.1997633  24.213  19.450   2.633  55.061
        Known (#4)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 10 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      4 missing connections, weight=     5015.0    
 decide> The unconnected minima in the chain and their distances are:
     2        8.10     7     7        1.53     5     6       15.59     9    10        8.83     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1743 Dev= 0.15% S= 8.22 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.21

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1055 steps. Energy=    -390.5554047       time=       2.61
 Minus side of path:                     970 steps. Energy=    -385.4120596       time=       2.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5554047  5.5869         -384.9684718 0.44359         -385.4120596  13.604  11.902   7.851  18.470
        Known (#8)                                              Known (#7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 5_U and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0116 Dev= 0.02% S= 1.53 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.54

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     937 steps. Energy=    -385.4005012       time=       2.12
 Minus side of path:                     931 steps. Energy=    -385.4120596       time=       2.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4005012 0.24639E-01     -385.3758621 0.36197E-01     -385.4120596   1.536   1.526   2.960  48.991
        Known (#5)                                              Known (#7)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 6_U and 9_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0226 Dev= 0.03% S= 15.64 time= 0.84
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   5.33

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     911 steps. Energy=    -388.6809028       time=       2.06
 Minus side of path:                     920 steps. Energy=    -388.5796269       time=       2.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6809028 0.14356         -388.5373394 0.42288E-01     -388.5796269  15.726  15.593   2.038  71.138
        Known (#6)                                              Known (#9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0681 Dev= 0.04% S= 8.89 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   5.12

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     967 steps. Energy=    -389.1997633       time=       2.23
 Minus side of path:                     988 steps. Energy=    -389.2335056       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1997633 0.47187E-01     -389.1525766 0.80929E-01     -389.2335056   9.519   8.834   5.441  26.650
        Known (#10)                                             Known (#1)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     955.23    
 decide> The unconnected minima in the chain and their distances are:
     2        7.82     5 
 

 tryconnect> 595-iteration DNEB run for minima 2_F and 5_S using 17 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 595 RMS= 0.0221 Dev= 4.21% S= 11.25 time= 13.54
 Following    2 images are candidates for TS:    3   15  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         15
 DNEB run yielded 2 true transition state(s) time=   5.39
 isnewts> transition state is the same as number        3 energy=     -384.9345330390
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     860 steps. Energy=    -389.1046918       time=       1.86
 Minus side of path:                     998 steps. Energy=    -390.5554047       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1046918 0.40270E-01     -389.0644215  1.4910         -390.5554047  13.831  12.858  10.498  13.812
        Known (#2)                                              Known (#8)

 >>>>>  Path run for ts 11 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     936 steps. Energy=    -385.4120596       time=       2.13
 Minus side of path:                    1059 steps. Energy=    -390.5554047       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4120596 0.47753         -384.9345330  5.6209         -390.5554047  13.459  11.905   7.860  18.447
        Known (#7)                                              Known (#8)
 Alternative path found between members of the S set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -389.2335056 0.80929E-01    -389.1525766 0.47187E-01    -389.1997633   9.519   8.834   5.441  26.650
   5     -389.1997633  1.4615        -387.7383072 0.64887        -388.3871812  24.213  19.450   2.633  55.061
   1     -388.3871812  3.7433        -384.6439207  3.5947        -388.2386015  47.259  42.195   3.256  44.536
   4     -388.2386015 0.87707        -387.3615291  1.2181        -388.5796269  14.127  13.006   2.084  69.585
   8     -388.5796269 0.42288E-01    -388.5373394 0.14356        -388.6809028  15.726  15.593   2.038  71.138
   2     -388.6809028  3.7826        -384.8983285 0.50217        -385.4005012  20.588  19.380   2.513  57.693
   7     -385.4005012 0.24639E-01    -385.3758621 0.36197E-01    -385.4120596   1.536   1.526   2.960  48.991
   3     -385.4120596 0.47753        -384.9345330  5.6209        -390.5554047  13.458  11.904   7.849  18.473
  10     -390.5554047  1.4910        -389.0644215 0.40270E-01    -389.1046918  13.831  12.858  10.498  13.812

 Number of TS in the path       =      9
 Number of cycles               =      4

 Elapsed time=                               140.95
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             54302 time=          72.26 %= 51.3
 OPTIM> # of energy+gradient+Hessian calls=       431 time=           1.98 %=  1.4
