
 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)@comp22.ch.
                 Created on  5/28/12 at 13: 7:32 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.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -386.9950363     RMS force=    0.9442932671E-06
 OPTIM> Final energy  =    -394.0946509     RMS force=    0.8441807438E-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=     77222.    
 decide> The unconnected minima in the chain and their distances are:
     2       42.58     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0906 Dev= 4.22% S= 50.86 time= 7.05
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        185
 DNEB run yielded 1 true transition state(s) time=  14.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1339 steps. Energy=    -397.5605733       time=       6.79
 Minus side of path:                     865 steps. Energy=    -388.6881227       time=       3.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5605733  8.9174         -388.6431809 0.44942E-01     -388.6881227  30.929  30.293   1.876  77.281
        *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=     32478.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.16     3     4       13.03     1 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 3_U using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0702 Dev= 2.17% S= 34.77 time= 4.10
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         62
 Converged to TS (number of iterations):         65
 DNEB run yielded 2 true transition state(s) time=  11.94

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     937 steps. Energy=    -396.2474142       time=       2.27
 Minus side of path:                     917 steps. Energy=    -394.0946509       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.2474142  2.2343         -394.0131071 0.81544E-01     -394.0946509  12.571  12.351   3.176  45.654
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1044 steps. Energy=    -397.5605733       time=       3.98
 Minus side of path:                     958 steps. Energy=    -396.2474142       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5605733  4.1193         -393.4412817  2.8061         -396.2474142  32.870  29.267   5.204  27.865
        Known (#3)                                              Known (#5)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4362 Dev= 0.97% S= 13.68 time= 0.50
 Following    2 images are candidates for TS:    1    3  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         43
 DNEB run yielded 2 true transition state(s) time=   9.40

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     917 steps. Energy=    -391.9281723       time=       3.47
 Minus side of path:                     947 steps. Energy=    -386.9950363       time=       3.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9281723  6.0192         -385.9089241  1.0861         -386.9950363   6.996   5.596  13.811  10.499
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1316 steps. Energy=    -393.7345412       time=       6.26
 Minus side of path:                     870 steps. Energy=    -388.6881227       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7345412  5.0792         -388.6553621 0.32761E-01     -388.6881227  23.247  21.772   2.253  64.363
        *NEW* (Placed in 7)                                     Known (#4)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1716.9    
 decide> The unconnected minima in the chain and their distances are:
     4       11.97     6 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 6_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1992 Dev= 0.34% S= 12.29 time= 0.49
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   6.59
 isnewts> transition state is the same as number        5 energy=     -388.6553620985
 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:                    1505 steps. Energy=    -397.5605733       time=       8.04
 Minus side of path:                     909 steps. Energy=    -388.6881227       time=       3.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5605733  8.9052         -388.6553621 0.32761E-01     -388.6881227  31.607  30.296   1.879  77.153
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3433.8    
 decide> The unconnected minima in the chain and their distances are:
     4       11.97     6 
 

 tryconnect> 805-iteration DNEB run for minima 4_F and 6_S using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 805 RMS= 0.4212 Dev= 4.31% S= 14.77 time= 28.90
 Following    2 images are candidates for TS:    3   10  
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         48
 DNEB run yielded 2 true transition state(s) time=  13.26
 isnewts> transition state is the same as number        1 energy=     -388.6431809016
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1334 steps. Energy=    -397.5605733       time=       6.31
 Minus side of path:                     875 steps. Energy=    -388.6881227       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5605733  8.9174         -388.6431809 0.44942E-01     -388.6881227  30.931  30.295   1.876  77.301
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1146 steps. Energy=    -393.7345412       time=       3.32
 Minus side of path:                     948 steps. Energy=    -389.6963819       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7345412  4.0913         -389.6432212 0.53161E-01     -389.6963819  18.832  18.027   3.632  39.920
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     231.09    
 decide> The unconnected minima in the chain and their distances are:
     8        6.14     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 8_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2020 Dev= 0.74% S= 6.45 time= 0.22
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   5.59

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     984 steps. Energy=    -393.7345412       time=       3.39
 Minus side of path:                     932 steps. Energy=    -389.6963819       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7345412  4.0990         -389.6355283 0.60854E-01     -389.6963819  18.649  18.029   3.721  38.972
        Known (#7)                                              Known (#8)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     387.81    
 decide> The unconnected minima in the chain and their distances are:
     8        7.29     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.3649 Dev= 0.63% S= 7.67 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.71

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     926 steps. Energy=    -390.5588080       time=       2.30
 Minus side of path:                     945 steps. Energy=    -387.3142778       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5588080  4.6394         -385.9193942  1.3949         -387.3142778   8.871   6.846  13.277  10.921
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     462.18    
 decide> The unconnected minima in the chain and their distances are:
     8        6.14     6 
 

 tryconnect> 490-iteration DNEB run for minima 6_S and 8_F using 14 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.168613344    
 Double-ended search iterations= 490 RMS= 0.2367 Dev= 35.59% S= 10.10 time= 10.12
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.87

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     927 steps. Energy=    -390.5588080       time=       3.36
 Minus side of path:                     955 steps. Energy=    -389.6963819       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5588080  3.4969         -387.0618596  2.6345         -389.6963819   8.667   8.054   6.803  21.314
        Known (#9)                                              Known (#8)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     32.137    
 decide> The unconnected minima in the chain and their distances are:
    10        3.18     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 10_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.3672 Dev= 2.20% S= 3.71 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   6.21

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     922 steps. Energy=    -386.9950363       time=       2.31
 Minus side of path:                     875 steps. Energy=    -386.9850276       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9950363 0.59597E-01     -386.9354394 0.49588E-01     -386.9850276   4.948   4.803   9.772  14.839
        Known (#1)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 11 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     54.759    
 decide> The unconnected minima in the chain and their distances are:
     9        3.80     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 9_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2549 Dev= 1.29% S= 4.17 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.70

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     909 steps. Energy=    -390.5588080       time=       2.50
 Minus side of path:                     924 steps. Energy=    -391.9281723       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5588080  5.1555         -385.4032692  6.5249         -391.9281723   5.388   3.798  29.830   4.861
        Known (#9)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -386.9950363  1.0861        -385.9089241  6.0192        -391.9281723   6.996   5.596  13.811  10.499
  13     -391.9281723  6.5249        -385.4032692  5.1555        -390.5588080   5.388   3.798  29.830   4.861
  11     -390.5588080  3.4969        -387.0618596  2.6345        -389.6963819   8.667   8.054   6.803  21.314
   8     -389.6963819 0.53161E-01    -389.6432212  4.0913        -393.7345412  18.832  18.027   3.632  39.920
   5     -393.7345412  5.0792        -388.6553621 0.32761E-01    -388.6881227  23.247  21.772   2.253  64.363
   1     -388.6881227 0.44942E-01    -388.6431809  8.9174        -397.5605733  30.929  30.293   1.876  77.281
   3     -397.5605733  4.1193        -393.4412817  2.8061        -396.2474142  32.870  29.267   5.204  27.865
   2     -396.2474142  2.2343        -394.0131071 0.81544E-01    -394.0946509  12.571  12.351   3.176  45.654

 Number of TS in the path       =      8
 Number of cycles               =      9

 Elapsed time=                               222.61
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             73469 time=         106.95 %= 48.0
 OPTIM> # of energy+gradient+Hessian calls=       701 time=           3.49 %=  1.6
