
 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)@comp35.ch.
                 Created on  5/28/12 at 12:38:47 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=    -391.1712673     RMS force=    0.9838863585E-06
 OPTIM> Final energy  =    -394.7678708     RMS force=    0.9471894182E-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=    0.22041E+06
 decide> The unconnected minima in the chain and their distances are:
     2       60.41     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 2_F using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 630 RMS= 0.0782 Dev= 4.86% S= 87.61 time= 16.15
 Following    2 images are candidates for TS:    3   12  
 Converged to TS (number of iterations):         42
 Converged to TS (number of iterations):        141
 DNEB run yielded 2 true transition state(s) time=  16.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     899 steps. Energy=    -392.7449319       time=       2.27
 Minus side of path:                     964 steps. Energy=    -391.1577527       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.7449319  4.6984         -388.0464856  3.1113         -391.1577527  32.628  31.124   1.841  78.763
        *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:                     896 steps. Energy=    -390.7995157       time=       3.61
 Minus side of path:                     927 steps. Energy=    -393.0415826       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7995157 0.22798         -390.5715311  2.4701         -393.0415826  17.510  16.445  10.708  13.541
        *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=     58941.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.17     5     6       35.01     4     3        4.56     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 5_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1002 Dev= 0.70% S= 27.03 time= 2.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        121
 DNEB run yielded 1 true transition state(s) time=  10.36
 isnewts> transition state is the same as number        2 energy=     -390.5715310688
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     897 steps. Energy=    -390.7995157       time=       2.15
 Minus side of path:                     942 steps. Energy=    -393.0415826       time=       2.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7995157 0.22798         -390.5715311  2.4701         -393.0415826  17.510  16.446  10.699  13.553
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 4_U and 6_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1497 Dev= 3.14% S= 39.70 time= 5.09
 Following    2 images are candidates for TS:    6    9  
 Converged to TS (number of iterations):         34
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         56
 DNEB run yielded 2 true transition state(s) time=  10.28

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     975 steps. Energy=    -392.0449973       time=       2.83
 Minus side of path:                     992 steps. Energy=    -391.7507267       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.0449973  3.8403         -388.2046636  3.5461         -391.7507267  40.257  35.826   2.005  72.310
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     956 steps. Energy=    -399.0761276       time=       3.49
 Minus side of path:                     879 steps. Energy=    -393.0415826       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -399.0761276  6.3180         -392.7580881 0.28349         -393.0415826  12.111  11.535  10.806  13.419
        *NEW* (Placed in 9)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2634 Dev= 1.15% S= 4.85 time= 0.27
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        187
 DNEB run yielded 1 true transition state(s) time=  21.46

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1252 steps. Energy=    -391.1712673       time=       3.87
 Minus side of path:                    1168 steps. Energy=    -392.2706816       time=       3.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1712673  2.8258         -388.3454851  3.9252         -392.2706816  31.625  27.768   7.097  20.430
        Known (#1)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      4 missing connections, weight=     23697.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.42     6     9        7.99     7     8        3.73     4     3        4.56     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 6_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.2439 Dev= 0.62% S= 30.42 time= 3.31
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):         20
 Converged to TS (number of iterations):         48
 DNEB run yielded 2 true transition state(s) time=   8.69

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     961 steps. Energy=    -392.8183303       time=       3.77
 Minus side of path:                     950 steps. Energy=    -395.4417387       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8183303 0.62939         -392.1889371  3.2528         -395.4417387  11.618  10.428   3.048  47.571
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     997 steps. Energy=    -392.8183303       time=       2.72
 Minus side of path:                    1001 steps. Energy=    -393.0109403       time=       3.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8183303  1.6986         -391.1197043  1.8912         -393.0109403  24.124  22.495   2.499  58.030
        Known (#11)                                             *NEW* (Placed in 13)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7695 Dev= 0.13% S= 8.09 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   5.40

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     842 steps. Energy=    -399.0761276       time=       2.23
 Minus side of path:                     923 steps. Energy=    -395.9761291       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -399.0761276  4.2221         -394.8540576  1.1221         -395.9761291   8.371   5.572  11.214  12.930
        Known (#9)                                              *NEW* (Placed in 14)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7798 Dev= 0.50% S= 3.79 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.29

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     884 steps. Energy=    -391.1159867       time=       3.55
 Minus side of path:                     873 steps. Energy=    -391.1577527       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1159867 0.32554E-01     -391.0834322 0.74320E-01     -391.1577527   1.180   1.167   5.808  24.967
        *NEW* (Placed in 15)                                    Known (#4)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 3_U using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3994903209    
 Double-ended search iterations= 350 RMS= 0.0322 Dev= 2.36% S= 8.21 time= 5.23
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.43

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     937 steps. Energy=    -392.7449319       time=       2.70
 Minus side of path:                     921 steps. Energy=    -391.1712673       time=       3.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.7449319  4.2402         -388.5046940  2.6666         -391.1712673  13.243   4.558  16.257   8.919
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 15 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     12 steps with      4 missing connections, weight=     639.46    
 decide> The unconnected minima in the chain and their distances are:
     2        5.50    12    13        5.90     6    14        5.98     7     8        3.77    15 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0765 Dev= 0.04% S= 5.53 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.30

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     934 steps. Energy=    -394.7678708       time=       2.91
 Minus side of path:                     937 steps. Energy=    -395.4417387       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.7678708 0.23315         -394.5347249 0.90701         -395.4417387   7.095   5.501   5.437  26.669
        Known (#2)                                              Known (#12)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 6_U and 13_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0555 Dev= 0.01% S= 5.91 time= 0.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.61

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     815 steps. Energy=    -393.0794579       time=       2.67
 Minus side of path:                     784 steps. Energy=    -393.0109403       time=       2.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0794579 0.94726E-01     -392.9847319 0.26208E-01     -393.0109403   1.668   1.658   9.318  15.562
        *NEW* (Placed in 16)                                    Known (#13)
 Unconnected minimum 16 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 14_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0604 Dev= 0.05% S= 6.01 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.14

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     912 steps. Energy=    -395.9761291       time=       2.40
 Minus side of path:                     856 steps. Energy=    -392.0449973       time=       2.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.9761291  3.9745         -392.0016768 0.43321E-01     -392.0449973   6.411   5.979   9.700  14.949
        Known (#14)                                             Known (#7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 15_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1358 Dev= 0.09% S= 3.80 time= 0.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.58

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     869 steps. Energy=    -391.1159867       time=       2.12
 Minus side of path:                     915 steps. Energy=    -391.7507267       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1159867 0.20077E-01     -391.0959095 0.65482         -391.7507267   4.118   3.774   3.497  41.468
        Known (#15)                                             Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 16 minima and 15 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     13 steps with      1 missing connections, weight=     136.94    
 decide> The unconnected minima in the chain and their distances are:
    16        5.15     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 16_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0246 Dev= 0.02% S= 5.16 time= 0.27
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.83

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     843 steps. Energy=    -393.0415826       time=       2.10
 Minus side of path:                     831 steps. Energy=    -393.0794579       time=       2.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0415826 0.83486E-01     -392.9580965 0.12136         -393.0794579   5.646   5.155   8.040  18.035
        Known (#6)                                              Known (#16)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  11     -391.1712673  2.6666        -388.5046940  4.2402        -392.7449319  13.243   4.558  16.257   8.919
   1     -392.7449319  4.6984        -388.0464856  3.1113        -391.1577527  32.628  31.124   1.841  78.763
  10     -391.1577527 0.74320E-01    -391.0834322 0.32554E-01    -391.1159867   1.180   1.167   5.808  24.967
  15     -391.1159867 0.20077E-01    -391.0959095 0.65482        -391.7507267   4.118   3.774   3.497  41.468
   4     -391.7507267  3.5461        -388.2046636  3.8403        -392.0449973  40.257  35.826   2.005  72.310
  14     -392.0449973 0.43321E-01    -392.0016768  3.9745        -395.9761291   6.411   5.979   9.700  14.949
   9     -395.9761291  1.1221        -394.8540576  4.2221        -399.0761276   8.371   5.572  11.214  12.930
   5     -399.0761276  6.3180        -392.7580881 0.28349        -393.0415826  12.111  11.535  10.806  13.419
  16     -393.0415826 0.83486E-01    -392.9580965 0.12136        -393.0794579   5.646   5.155   8.040  18.035
  13     -393.0794579 0.94726E-01    -392.9847319 0.26208E-01    -393.0109403   1.668   1.658   9.318  15.562
   8     -393.0109403  1.8912        -391.1197043  1.6986        -392.8183303  24.124  22.495   2.499  58.030
   7     -392.8183303 0.62939        -392.1889371  3.2528        -395.4417387  11.618  10.428   3.048  47.571
  12     -395.4417387 0.90701        -394.5347249 0.23315        -394.7678708   7.095   5.501   5.437  26.669

 Number of TS in the path       =     13
 Number of cycles               =      5

 Elapsed time=                               226.17
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             68690 time=          97.64 %= 43.2
 OPTIM> # of energy+gradient+Hessian calls=       828 time=           4.36 %=  1.9
