
 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)@comp32.ch.
                 Created on  5/28/12 at 12:47:17 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=    -381.7654884     RMS force=    0.8830557765E-06
 OPTIM> Final energy  =    -378.7713696     RMS force=    0.8923153024E-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=    0.10210E+06
 decide> The unconnected minima in the chain and their distances are:
     2       46.74     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      495.6144107    
 Double-ended search iterations= 587 RMS= 2.3623 Dev= 0.13% S= 48.00 time= 11.17
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        170
 DNEB run yielded 1 true transition state(s) time=  15.29

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     932 steps. Energy=    -378.5378511       time=       3.14
 Minus side of path:                    1030 steps. Energy=    -384.1515345       time=       4.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.5378511 0.79041E-01     -378.4588096  5.6927         -384.1515345  20.666  19.333   6.787  21.364
        *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=     46903.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.81     3     3       28.43     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      153.6741246    
 Double-ended search iterations= 280 RMS= 11.6534 Dev= 19.99% S= 35.26 time= 3.05
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        127
 DNEB run yielded 1 true transition state(s) time=   9.37

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1025 steps. Energy=    -378.5010307       time=       3.27
 Minus side of path:                    1148 steps. Energy=    -384.5231228       time=       4.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.5010307  2.4575         -376.0435371  8.4796         -384.5231228  39.860  35.635   2.561  56.625
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 280 RMS= 4.2053 Dev= 0.88% S= 29.31 time= 3.04
 Following    4 images are candidates for TS:    2    4    6    8  
 Converged to TS (number of iterations):        165
 Converged to TS (number of iterations):        122
 Converged to TS (number of iterations):        108
 Converged to TS (number of iterations):         20
 DNEB run yielded 4 true transition state(s) time=  48.94
 isnewts> transition state is the same as number        3 energy=     -380.4061323191
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1058 steps. Energy=    -381.7654884       time=       3.18
 Minus side of path:                     964 steps. Energy=    -380.4213528       time=       2.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7654884  1.3594         -380.4061323 0.15220E-01     -380.4213528  19.522  19.268   2.518  57.583
        Known (#1)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to S set.

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     949 steps. Energy=    -381.7654884       time=       2.60
 Minus side of path:                     943 steps. Energy=    -380.4213528       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7654884  1.3594         -380.4061323 0.15220E-01     -380.4213528  19.518  19.264   2.532  57.271
        Known (#1)                                              Known (#7)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1112 steps. Energy=    -381.7654884       time=       4.22
 Minus side of path:                    1064 steps. Energy=    -386.4567933       time=       4.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7654884  2.9552         -378.8102945  7.6465         -386.4567933  45.125  36.687   3.566  40.664
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1205 steps. Energy=    -381.7654884       time=       5.12
 Minus side of path:                     970 steps. Energy=    -378.5378511       time=       2.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7654884  3.2787         -378.4867698 0.51081E-01     -378.5378511  28.832  28.470   3.668  39.536
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     5686.0    
 decide> The unconnected minima in the chain and their distances are:
     2       16.55     5     6       10.50     4 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 5_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 0.1469 Dev= 0.34% S= 16.62 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   5.51

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1020 steps. Energy=    -379.0114533       time=       4.02
 Minus side of path:                     930 steps. Energy=    -378.5010307       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.0114533  1.0556         -377.9558608 0.54517         -378.5010307  10.138   8.408   2.174  66.703
        *NEW* (Placed in 9)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_S and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 0.3602 Dev= 0.70% S= 10.73 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   6.03

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     952 steps. Energy=    -391.0262250       time=       3.23
 Minus side of path:                     944 steps. Energy=    -384.1515345       time=       3.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.0262250  8.0285         -382.9977259  1.1538         -384.1515345  11.555   8.419  22.167   6.541
        *NEW* (Placed in 10)                                    Known (#4)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     2480.1    
 decide> The unconnected minima in the chain and their distances are:
     2       12.94     9     6        6.78    10 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 9_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 0.1417 Dev= 0.16% S= 12.97 time= 0.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   5.51

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     925 steps. Energy=    -379.0114533       time=       3.83
 Minus side of path:                     941 steps. Energy=    -378.7527252       time=       3.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.0114533 0.29422         -378.7172380 0.35487E-01     -378.7527252   6.173   6.027   3.439  42.161
        Known (#9)                                              *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 6_U and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.1790 Dev= 0.84% S= 6.92 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        183
 DNEB run yielded 1 true transition state(s) time=  19.67

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     954 steps. Energy=    -388.5125165       time=       3.53
 Minus side of path:                     935 steps. Energy=    -387.8412847       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5125165  3.7828         -384.7297055  3.1116         -387.8412847  37.486  33.341   1.736  83.523
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      3 missing connections, weight=     1633.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.85    11     6        6.68    12    12        3.84    10 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 11_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.0685 Dev= 0.20% S= 10.89 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.96

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     959 steps. Energy=    -378.7527252       time=       2.88
 Minus side of path:                     983 steps. Energy=    -378.7713696       time=       3.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.7527252 0.82059E-01     -378.6706658 0.10070         -378.7713696  11.125  10.856  13.191  10.993
        Known (#11)                                             Known (#2)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 6_F and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0867 Dev= 0.43% S= 6.72 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   7.11

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     931 steps. Energy=    -384.5231228       time=       3.42
 Minus side of path:                     936 steps. Energy=    -384.7658225       time=       2.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.5231228 0.10426         -384.4188620 0.34696         -384.7658225   7.793   6.978   6.664  21.758
        Known (#6)                                              *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 10_S and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.1544 Dev= 0.54% S= 3.91 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.90

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     837 steps. Energy=    -388.5125165       time=       2.19
 Minus side of path:                     910 steps. Energy=    -391.0262250       time=       2.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5125165 0.42052         -388.0919971  2.9342         -391.0262250   3.981   3.838  11.009  13.171
        Known (#12)                                             Known (#10)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 14 minima and 13 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     421.80    
 decide> The unconnected minima in the chain and their distances are:
    14        7.50    12 
 

 tryconnect> 70-iteration DNEB run for minima 12_S and 14_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0618 Dev= 0.21% S= 7.52 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     897 steps. Energy=    -384.7658225       time=       3.12
 Minus side of path:                     904 steps. Energy=    -388.5125165       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.7658225 0.71594E-01     -384.6942282  3.8183         -388.5125165   7.631   7.500  12.246  11.841
        Known (#14)                                             Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -381.7654884  3.2787        -378.4867698 0.51081E-01    -378.5378511  28.832  28.470   3.668  39.536
   1     -378.5378511 0.79041E-01    -378.4588096  5.6927        -384.1515345  20.666  19.333   6.787  21.364
   8     -384.1515345  1.1538        -382.9977259  8.0285        -391.0262250  11.555   8.419  22.167   6.541
  13     -391.0262250  2.9342        -388.0919971 0.42052        -388.5125165   3.981   3.838  11.009  13.171
  14     -388.5125165  3.8183        -384.6942282 0.71594E-01    -384.7658225   7.631   7.500  12.246  11.841
  12     -384.7658225 0.34696        -384.4188620 0.10426        -384.5231228   7.793   6.978   6.664  21.758
   2     -384.5231228  8.4796        -376.0435371  2.4575        -378.5010307  39.860  35.635   2.561  56.625
   7     -378.5010307 0.54517        -377.9558608  1.0556        -379.0114533  10.138   8.408   2.174  66.703
   9     -379.0114533 0.29422        -378.7172380 0.35487E-01    -378.7527252   6.173   6.027   3.439  42.161
  11     -378.7527252 0.82059E-01    -378.6706658 0.10070        -378.7713696  11.125  10.856  13.191  10.993

 Number of TS in the path       =     10
 Number of cycles               =      6

 Elapsed time=                               241.12
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             58789 time=          79.25 %= 32.9
 OPTIM> # of energy+gradient+Hessian calls=      1134 time=           5.86 %=  2.4
