
 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 12:47:47 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -392.6100209     RMS force=    0.9802682475E-06
 OPTIM> Final energy  =    -389.6911464     RMS force=    0.8247176248E-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=     6430.8    
 decide> The unconnected minima in the chain and their distances are:
     2       18.60     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 175 RMS= 5.4741 Dev= 18.96% S= 19.15 time= 1.19
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        231
 DNEB run yielded 1 true transition state(s) time=  23.72

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1062 steps. Energy=    -390.3256659       time=       3.41
 Minus side of path:                    1017 steps. Energy=    -389.1185940       time=       3.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3256659  4.2536         -386.0720312  3.0466         -389.1185940  31.116  24.910   3.156  45.938
        *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=     4971.5    
 decide> The unconnected minima in the chain and their distances are:
     2        6.48     4     4       16.75     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      16.28894627    
 Double-ended search iterations= 70 RMS= 1.8476 Dev= 1.12% S= 7.40 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   4.48

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     852 steps. Energy=    -389.6911464       time=       2.69
 Minus side of path:                     846 steps. Energy=    -389.7036477       time=       2.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6911464 0.47586E-01     -389.6435609 0.60087E-01     -389.7036477   0.776   0.772  26.271   5.519
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      18.85649142    
 Double-ended search iterations= 175 RMS= 0.7112 Dev= 0.92% S= 16.89 time= 1.21
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        247
 DNEB run yielded 1 true transition state(s) time=  29.29
 isnewts> transition state is the same as number        1 energy=     -386.0720311795
 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:                    1090 steps. Energy=    -390.3256659       time=       5.07
 Minus side of path:                    1699 steps. Energy=    -390.7486831       time=      10.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3256659  4.2536         -386.0720312  4.6767         -390.7486831  51.526  34.119   2.560  56.641
        Known (#3)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6506.0    
 decide> The unconnected minima in the chain and their distances are:
     5       18.67     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      33.86354941    
 Double-ended search iterations= 175 RMS= 0.5459 Dev= 1.24% S= 18.80 time= 1.19
 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=  22.32
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     9673.2    
 decide> The unconnected minima in the chain and their distances are:
     5        6.50     4     4       16.75     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      16.28894627    
 Double-ended search iterations= 70 RMS= 4.1228 Dev= 3.44% S= 7.44 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.20

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     946 steps. Energy=    -389.1185940       time=       2.80
 Minus side of path:                     926 steps. Energy=    -389.1273750       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1185940 0.56581E-02     -389.1129359 0.14439E-01     -389.1273750   0.837   0.834   4.133  35.087
        Known (#4)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4194648369    
 Double-ended search iterations= 805 RMS= 0.0259 Dev= 3.35% S= 21.74 time= 24.90
 Following    1 images are candidates for TS:   21  
 Converged to TS (number of iterations):        141
 DNEB run yielded 1 true transition state(s) time=  17.09

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1329 steps. Energy=    -390.7486831       time=       4.29
 Minus side of path:                    1027 steps. Energy=    -395.9937664       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7486831  1.5139         -389.2347487  6.7590         -395.9937664  39.425  34.895   1.950  74.374
        Known (#6)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     5111.7    
 decide> The unconnected minima in the chain and their distances are:
     2        6.42     7     7       16.92     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      14.77455444    
 Double-ended search iterations= 70 RMS= 0.6193 Dev= 1.48% S= 7.31 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        136
 DNEB run yielded 1 true transition state(s) time=  11.74

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1049 steps. Energy=    -389.6911464       time=       3.72
 Minus side of path:                     934 steps. Energy=    -387.3144327       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6911464  2.6579         -387.0332386 0.28119         -387.3144327  20.881  20.379   3.005  48.248
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 7_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 175 RMS= 1.0349 Dev= 1.04% S= 17.10 time= 1.20
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        165
 DNEB run yielded 1 true transition state(s) time=  18.20

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     920 steps. Energy=    -389.7214727       time=       2.20
 Minus side of path:                    1469 steps. Energy=    -392.6100209       time=       5.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7214727  3.3834         -386.3380917  6.2719         -392.6100209  34.894  31.788   7.945  18.250
        *NEW* (Placed in 10)                                    Known (#1)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     9958.8    
 decide> The unconnected minima in the chain and their distances are:
     5        6.43     7     7       16.92     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 70 RMS= 0.8709 Dev= 2.56% S= 7.32 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   3.80
 isnewts> transition state is the same as number        4 energy=     -389.1129358931
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     952 steps. Energy=    -389.1185940       time=       2.30
 Minus side of path:                     935 steps. Energy=    -389.1273750       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1185940 0.56581E-02     -389.1129359 0.14439E-01     -389.1273750   0.837   0.834   4.133  35.087
        Known (#4)                                              Known (#7)
 Connection established between members of the U set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 7_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 805 RMS= 0.0323 Dev= 2.73% S= 21.68 time= 25.55
 Following    1 images are candidates for TS:   21  
 Converged to TS (number of iterations):        195
 DNEB run yielded 1 true transition state(s) time=  28.71
 isnewts> transition state is the same as number        1 energy=     -386.0720311795
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     12635.    
 decide> The unconnected minima in the chain and their distances are:
     2        6.42     7     3       22.96     1 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 7_U using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 490 RMS= 0.0858 Dev= 3.08% S= 9.22 time= 9.29
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   5.11

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1129 steps. Energy=    -389.6911464       time=       3.67
 Minus side of path:                    1477 steps. Energy=    -390.7486831       time=       5.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6911464  2.8182         -386.8729127  3.8758         -390.7486831  44.454  34.335   2.010  72.153
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 3_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 210 RMS= 0.4090 Dev= 0.70% S= 25.72 time= 1.75
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   7.89

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     965 steps. Energy=    -392.6253419       time=       2.78
 Minus side of path:                    1054 steps. Energy=    -390.7486831       time=       3.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.6253419  2.7886         -389.8367744 0.91191         -390.7486831  21.564  20.034   2.827  51.290
        *NEW* (Placed in 11)                                    Known (#6)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     745.52    
 decide> The unconnected minima in the chain and their distances are:
    11        9.07     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 11_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.2695 Dev= 0.24% S= 9.09 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   6.53

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     922 steps. Energy=    -392.6100209       time=       3.77
 Minus side of path:                     922 steps. Energy=    -392.6253419       time=       2.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.6100209 0.68684         -391.9231777 0.70216         -392.6253419  14.946   9.085   2.228  65.089
        Known (#1)                                              Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  11     -392.6100209 0.68684        -391.9231777 0.70216        -392.6253419  14.946   9.085   2.228  65.089
  10     -392.6253419  2.7886        -389.8367744 0.91191        -390.7486831  21.564  20.034   2.827  51.290
   9     -390.7486831  3.8758        -386.8729127  2.8182        -389.6911464  44.454  34.335   2.010  72.153

 Number of TS in the path       =      3
 Number of cycles               =      8

 Elapsed time=                               331.10
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             92411 time=         123.23 %= 37.2
 OPTIM> # of energy+gradient+Hessian calls=      1607 time=           8.21 %=  2.5
