
 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)@comp24.ch.
                 Created on  5/28/12 at 12:49:14 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=    -386.1053788     RMS force=    0.9501329568E-06
 OPTIM> Final energy  =    -396.8219334     RMS force=    0.7851346602E-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=     52419.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.43     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.1206 Dev= 2.52% S= 46.06 time= 5.77
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        178
 DNEB run yielded 1 true transition state(s) time=  17.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1234 steps. Energy=    -392.4385271       time=       4.79
 Minus side of path:                     974 steps. Energy=    -387.3873906       time=       3.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4385271  5.2127         -387.2258737 0.16152         -387.3873906  22.719  19.803   3.110  46.629
        *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=     87682.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.15     4     4       41.56     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0996 Dev= 0.96% S= 29.20 time= 2.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.44

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1106 steps. Energy=    -387.3873906       time=       4.00
 Minus side of path:                     962 steps. Energy=    -387.2405770       time=       3.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3873906  3.3009         -384.0864600  3.1541         -387.2405770  24.000  21.289   6.147  23.590
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 420-iteration DNEB run for minima 1_S and 4_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0454 Dev= 2.38% S= 49.59 time= 6.97
 Following    2 images are candidates for TS:    3   12  
 Converged to TS (number of iterations):         49
 Converged to TS (number of iterations):         25
 DNEB run yielded 2 true transition state(s) time=   9.12

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     965 steps. Energy=    -385.9147220       time=       2.29
 Minus side of path:                     987 steps. Energy=    -386.1053788       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9147220 0.19669         -385.7180324 0.38735         -386.1053788  17.689  16.887   3.996  36.290
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     943 steps. Energy=    -387.3873906       time=       2.22
 Minus side of path:                    1038 steps. Energy=    -390.3044736       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3873906 0.24077E-01     -387.3633140  2.9412         -390.3044736  16.890  16.370   2.329  62.246
        Known (#4)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     18612.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.74     5     5       26.05     6 
 

 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= 0.7346 Dev= 0.95% S= 10.81 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        118
 DNEB run yielded 1 true transition state(s) time=   7.87

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     923 steps. Energy=    -388.5631391       time=       2.18
 Minus side of path:                     927 steps. Energy=    -387.2405770       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5631391  1.5769         -386.9862173 0.25436         -387.2405770   8.130   7.123   5.131  28.257
        *NEW* (Placed in 8)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 5_U and 6_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2336 Dev= 0.26% S= 27.19 time= 2.30
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        128
 DNEB run yielded 1 true transition state(s) time=   8.75

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1120 steps. Energy=    -388.4421440       time=       2.99
 Minus side of path:                    1153 steps. Energy=    -389.9957168       time=       3.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4421440  2.2340         -386.2081421  3.7876         -389.9957168  29.436  21.043   7.083  20.470
        *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      5 steps with      3 missing connections, weight=     21465.    
 decide> The unconnected minima in the chain and their distances are:
     2       10.05     8     8        7.31     9    10       27.17     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.6153 Dev= 1.96% S= 10.69 time= 0.45
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    3  
 Converged to TS (number of iterations):         82
 DNEB run yielded 1 true transition state(s) time=   6.21

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     926 steps. Energy=    -397.1770852       time=       2.20
 Minus side of path:                     972 steps. Energy=    -396.8219334       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.1770852  2.1269         -395.0502238  1.7717         -396.8219334  18.142  17.573   3.642  39.810
        *NEW* (Placed in 11)                                    Known (#2)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.3332 Dev= 2.78% S= 7.67 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.20

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     867 steps. Energy=    -388.5691851       time=       1.94
 Minus side of path:                     886 steps. Energy=    -388.5631391       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5691851 0.56192E-01     -388.5129926 0.50147E-01     -388.5631391   1.089   1.080   6.007  24.140
        *NEW* (Placed in 12)                                    Known (#8)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 6_S and 10_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0501 Dev= 0.46% S= 28.47 time= 3.04
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   4.90

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     902 steps. Energy=    -385.9147220       time=       1.98
 Minus side of path:                    1203 steps. Energy=    -390.3044736       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9147220 0.20461E-02     -385.9126758  4.3918         -390.3044736  29.905  29.576   1.926  75.269
        Known (#6)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1184.1    
 decide> The unconnected minima in the chain and their distances are:
     2       10.58    12 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 12_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3142 Dev= 1.64% S= 11.13 time= 0.44
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    3  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=   7.35
 isnewts> transition state is the same as number        7 energy=     -395.0502237881
 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:                     920 steps. Energy=    -397.1770852       time=       2.16
 Minus side of path:                     990 steps. Energy=    -396.8219334       time=       2.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.1770852  2.1269         -395.0502238  1.7717         -396.8219334  18.141  17.572   3.647  39.758
        Known (#11)                                             Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1849.3    
 decide> The unconnected minima in the chain and their distances are:
     2        9.74     5 
 

 tryconnect> 770-iteration DNEB run for minima 2_F and 5_S using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4855829818    
 Double-ended search iterations= 770 RMS= 0.0211 Dev= 4.74% S= 18.38 time= 23.56
 Following    2 images are candidates for TS:   13   21  
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):         15
 DNEB run yielded 2 true transition state(s) time=   6.04
 isnewts> transition state is the same as number        5 energy=     -386.9862172717
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     925 steps. Energy=    -388.5631391       time=       2.13
 Minus side of path:                     971 steps. Energy=    -396.8219334       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5631391 0.19154         -388.3715992  8.4503         -396.8219334  12.238  10.053   5.445  26.631
        Known (#8)                                              Known (#2)

 >>>>>  Path run for ts 12 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     950 steps. Energy=    -388.5631391       time=       2.22
 Minus side of path:                     943 steps. Energy=    -387.2405770       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5631391  1.5769         -386.9862173 0.25436         -387.2405770   8.130   7.123   5.131  28.260
        Known (#8)                                              Known (#5)
 Alternative path found between members of the S set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -386.1053788 0.38735        -385.7180324 0.19669        -385.9147220  17.689  16.887   3.996  36.290
   9     -385.9147220 0.20461E-02    -385.9126758  4.3918        -390.3044736  29.905  29.576   1.926  75.269
   4     -390.3044736  2.9412        -387.3633140 0.24077E-01    -387.3873906  16.890  16.370   2.329  62.246
   2     -387.3873906  3.3009        -384.0864600  3.1541        -387.2405770  24.000  21.289   6.147  23.590
   5     -387.2405770 0.25436        -386.9862173  1.5769        -388.5631391   8.130   7.123   5.131  28.257
  11     -388.5631391 0.19154        -388.3715992  8.4503        -396.8219334  12.238  10.053   5.445  26.631

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

 Elapsed time=                               185.98
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             68861 time=          93.00 %= 50.0
 OPTIM> # of energy+gradient+Hessian calls=       861 time=           3.72 %=  2.0
