
 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)@comp26.ch.
                 Created on  5/28/12 at 12:44:40 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=    -399.4433289     RMS force=    0.8667251535E-06
 OPTIM> Final energy  =    -388.3743583     RMS force=    0.9589739517E-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=     84690.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.91     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0855 Dev= 1.99% S= 52.17 time= 8.20
 Following    2 images are candidates for TS:    8   12  
 Converged to TS (number of iterations):        118
 Converged to TS (number of iterations):         19
 DNEB run yielded 2 true transition state(s) time=  16.30

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     934 steps. Energy=    -397.9716366       time=       3.44
 Minus side of path:                     907 steps. Energy=    -396.1464806       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.9716366  2.4840         -395.4876488 0.65883         -396.1464806   7.632   7.478   9.144  15.858
        *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:                    1202 steps. Energy=    -394.3983805       time=       5.15
 Minus side of path:                     926 steps. Energy=    -388.3743583       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.3983805  6.3778         -388.0205580 0.35380         -388.3743583  29.209  27.402   1.975  73.411
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     13990.    
 decide> The unconnected minima in the chain and their distances are:
     5       24.09     4     4        2.33     1 
 

 tryconnect> 245-iteration DNEB run for minima 4_U and 5_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0803 Dev= 0.45% S= 25.62 time= 2.42
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.64

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     917 steps. Energy=    -394.3983805       time=       2.50
 Minus side of path:                    1154 steps. Energy=    -397.6033483       time=       4.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.3983805  2.2574         -392.1410102  5.4623         -397.6033483  25.872  23.055   2.355  61.561
        Known (#5)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.3079 Dev= 7.83% S= 2.77 time= 0.21
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   7.21

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     903 steps. Energy=    -396.1464806       time=       3.52
 Minus side of path:                     897 steps. Energy=    -395.5808440       time=       3.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806 0.62768         -395.5187971 0.62047E-01     -395.5808440  10.469  10.131   5.565  26.055
        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      5 steps with      2 missing connections, weight=     1001.3    
 decide> The unconnected minima in the chain and their distances are:
     6        9.92     3     4        2.33     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0964 Dev= 0.01% S= 9.94 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        107
 DNEB run yielded 1 true transition state(s) time=  10.96

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     874 steps. Energy=    -397.5322550       time=       2.89
 Minus side of path:                    1030 steps. Energy=    -397.9716366       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5322550 0.59115         -396.9411086  1.0305         -397.9716366  15.018  13.898   2.547  56.920
        *NEW* (Placed in 8)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 175 RMS= 0.1080 Dev= 4.84% S= 2.92 time= 1.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.28

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     876 steps. Energy=    -396.1464806       time=       3.03
 Minus side of path:                     833 steps. Energy=    -399.4433289       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  3.7716         -392.3749287  7.0684         -399.4433289   4.422   2.329  35.211   4.118
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     241.58    
 decide> The unconnected minima in the chain and their distances are:
     6        6.23     8 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0976 Dev= 0.03% S= 6.25 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   6.83
 isnewts> transition state is the same as number        5 energy=     -396.9411086295
 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:                     897 steps. Energy=    -397.5322550       time=       3.53
 Minus side of path:                    1060 steps. Energy=    -397.9716366       time=       4.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5322550 0.59115         -396.9411086  1.0305         -397.9716366  15.018  13.898   2.547  56.934
        Known (#8)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     483.16    
 decide> The unconnected minima in the chain and their distances are:
     6        6.23     8 
 

 tryconnect> 490-iteration DNEB run for minima 6_F and 8_S using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 490 RMS= 0.0064 Dev= 5.19% S= 8.03 time= 9.65
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.79
 isnewts> transition state is the same as number        5 energy=     -396.9411086293
 tryconnect> Will not repeat search for TS      1 same as TS      5
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     724.74    
 decide> The unconnected minima in the chain and their distances are:
     6        6.23     8 
 

 tryconnect> 805-iteration DNEB run for minima 6_F and 8_S using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant     0.2575150228    
 Double-ended search iterations= 805 RMS= 0.0043 Dev= 5.36% S= 8.52 time= 26.01
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.85
 isnewts> transition state is the same as number        5 energy=     -396.9411086293
 tryconnect> Will not repeat search for TS      1 same as TS      5
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1079.4    
 decide> The unconnected minima in the chain and their distances are:
     6       10.26     7 
 

 tryconnect> 105-iteration DNEB run for minima 6_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1011 Dev= 0.31% S= 10.44 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   4.35

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1043 steps. Energy=    -396.1464806       time=       2.60
 Minus side of path:                    1076 steps. Energy=    -397.9716366       time=       2.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  1.0069         -395.1395357  2.8321         -397.9716366  23.256   7.485   9.575  15.143
        Known (#4)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1735.4    
 decide> The unconnected minima in the chain and their distances are:
     6       12.02     4 
 

 tryconnect> 105-iteration DNEB run for minima 4_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1605 Dev= 0.40% S= 12.22 time= 0.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.41
 isnewts> transition state is the same as number        1 energy=     -395.4876487504
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     894 steps. Energy=    -396.1464806       time=       2.27
 Minus side of path:                     932 steps. Energy=    -397.9716366       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806 0.65883         -395.4876488  2.4840         -397.9716366   7.633   7.478   9.134  15.874
        Known (#4)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 8 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1952.2    
 decide> The unconnected minima in the chain and their distances are:
     6        9.92     3 
 

 tryconnect> 770-iteration DNEB run for minima 3_S and 6_F using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1070028109    
 Double-ended search iterations= 659 RMS= 0.0010 Dev= 4.45% S= 10.54 time= 20.00
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:   22  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        211
 DNEB run yielded 1 true transition state(s) time=  14.39

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1083 steps. Energy=    -397.5139278       time=       2.91
 Minus side of path:                     886 steps. Energy=    -394.5320868       time=       2.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5139278  4.8671         -392.6467811  1.8853         -394.5320868  29.322  26.385  12.298  11.790
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 10 minima and 10 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     239.44    
 decide> The unconnected minima in the chain and their distances are:
     6        6.19     9     9        1.24     8 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0662 Dev= 0.04% S= 6.21 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=   3.30

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     932 steps. Energy=    -397.6033483       time=       2.16
 Minus side of path:                     923 steps. Energy=    -397.5139278       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.6033483 0.68618         -396.9171694 0.59676         -397.5139278   7.484   6.193   2.835  51.153
        Known (#6)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0286 Dev= 0.09% S= 1.25 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.43

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     903 steps. Energy=    -397.5139278       time=       2.07
 Minus side of path:                     881 steps. Energy=    -397.5322550       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5139278 0.38865E-01     -397.4750629 0.57192E-01     -397.5322550   1.244   1.242   4.239  34.205
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -399.4433289  7.0684        -392.3749287  3.7716        -396.1464806   4.422   2.329  35.211   4.118
   1     -396.1464806 0.65883        -395.4876488  2.4840        -397.9716366   7.632   7.478   9.144  15.858
   5     -397.9716366  1.0305        -396.9411086 0.59115        -397.5322550  15.018  13.898   2.547  56.920
  12     -397.5322550 0.57192E-01    -397.4750629 0.38865E-01    -397.5139278   1.244   1.242   4.239  34.205
  11     -397.5139278 0.59676        -396.9171694 0.68618        -397.6033483   7.484   6.193   2.835  51.153
   3     -397.6033483  5.4623        -392.1410102  2.2574        -394.3983805  25.872  23.055   2.355  61.561
   2     -394.3983805  6.3778        -388.0205580 0.35380        -388.3743583  29.209  27.402   1.975  73.411

 Number of TS in the path       =      7
 Number of cycles               =     10

 Elapsed time=                               225.53
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             86905 time=         117.66 %= 52.2
 OPTIM> # of energy+gradient+Hessian calls=       768 time=           3.81 %=  1.7
