
 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)@comp33.ch.
                 Created on  5/28/12 at 12:52:25 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=    -392.0442402     RMS force=    0.9657448806E-06
 OPTIM> Final energy  =    -394.5236511     RMS force=    0.9926872074E-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=     25566.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.46     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.059966752    
 Double-ended search iterations= 280 RMS= 0.3791 Dev= 2.14% S= 35.87 time= 3.17
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   4.70

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     923 steps. Energy=    -388.9942221       time=       2.74
 Minus side of path:                     941 steps. Energy=    -389.2768969       time=       4.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9942221  2.9159         -386.0783017  3.1986         -389.2768969   7.629   7.061  23.758   6.103
        *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=     6143.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.01     3     4       12.68     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2537 Dev= 1.39% S= 17.86 time= 0.82
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   5.94

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1137 steps. Energy=    -391.7303635       time=       4.12
 Minus side of path:                     931 steps. Energy=    -389.2768969       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7303635  4.1879         -387.5424931  1.7344         -389.2768969  31.847  28.297  12.954  11.194
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2092 Dev= 0.63% S= 13.40 time= 0.43
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  64.90
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     5909.4    
 decide> The unconnected minima in the chain and their distances are:
     2       12.24     5     4       12.68     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3460 Dev= 0.55% S= 12.96 time= 0.45
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.64

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 805 RMS= 0.0879 Dev= 5.89% S= 18.24 time= 25.54
 Following    2 images are candidates for TS:   10   21  
 Converged to TS (number of iterations):         34
 Converged to TS (number of iterations):         18
 DNEB run yielded 2 true transition state(s) time=   8.29

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     956 steps. Energy=    -392.0442402       time=       3.54
 Minus side of path:                     946 steps. Energy=    -392.7078534       time=       3.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.0442402  2.4669         -389.5773618  3.1305         -392.7078534   5.892   4.982  35.152   4.125
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     982 steps. Energy=    -391.7220965       time=       3.49
 Minus side of path:                     940 steps. Energy=    -389.2768969       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7220965  3.0864         -388.6357456 0.64115         -389.2768969  10.793   9.596  23.760   6.103
        *NEW* (Placed in 7)                                     Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     3769.1    
 decide> The unconnected minima in the chain and their distances are:
     2       12.24     5     7        4.71     1 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 5_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 805 RMS= 0.0763 Dev= 4.26% S= 16.94 time= 25.48
 Following    2 images are candidates for TS:   10   21  
 Converged to TS (number of iterations):        209
 Converged to TS (number of iterations):         20
 DNEB run yielded 2 true transition state(s) time=  25.43

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     937 steps. Energy=    -392.7078534       time=       3.02
 Minus side of path:                    1305 steps. Energy=    -395.3368184       time=       4.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.7078534  3.6691         -389.0387984  6.2980         -395.3368184  50.514  32.867  10.992  13.192
        Known (#6)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     942 steps. Energy=    -391.7303635       time=       2.29
 Minus side of path:                     962 steps. Energy=    -394.1237342       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7303635 0.55370         -391.1766617  2.9471         -394.1237342   8.875   7.558  24.357   5.953
        Known (#5)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8542 Dev= 0.50% S= 5.23 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        159
 DNEB run yielded 1 true transition state(s) time=  12.23

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1483 steps. Energy=    -395.1959889       time=       7.28
 Minus side of path:                    1299 steps. Energy=    -396.9746525       time=       5.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.1959889  9.4794         -385.7166043  11.258         -396.9746525  59.859  32.887   6.153  23.565
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     225.28    
 decide> The unconnected minima in the chain and their distances are:
     2        6.08     8 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5218 Dev= 0.31% S= 6.50 time= 0.21
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  27.66
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     450.56    
 decide> The unconnected minima in the chain and their distances are:
     2        6.08     8 
 

 tryconnect> 455-iteration DNEB run for minima 2_F and 8_S using 13 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0089 Dev= 2.26% S= 8.97 time= 8.22
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   4.48

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     942 steps. Energy=    -394.5236511       time=       2.86
 Minus side of path:                     939 steps. Energy=    -395.3368184       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.5236511  2.4930         -392.0306981  3.3061         -395.3368184   7.181   6.087  32.662   4.439
        Known (#2)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -392.0442402  2.4669        -389.5773618  3.1305        -392.7078534   5.892   4.982  35.152   4.125
   5     -392.7078534  3.6691        -389.0387984  6.2980        -395.3368184  50.514  32.867  10.992  13.192
   8     -395.3368184  3.3061        -392.0306981  2.4930        -394.5236511   7.181   6.087  32.662   4.439

 Number of TS in the path       =      3
 Number of cycles               =      6

 Elapsed time=                               300.58
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             80485 time=         109.06 %= 36.3
 OPTIM> # of energy+gradient+Hessian calls=      1265 time=           6.69 %=  2.2
