
 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)@comp29.ch.
                 Created on  5/28/12 at 12:57:45 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=    -391.8645413     RMS force=    0.8849644293E-06
 OPTIM> Final energy  =    -379.0342386     RMS force=    0.8130659390E-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=    0.15540E+06
 decide> The unconnected minima in the chain and their distances are:
     2       53.76     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 2_F using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 560 RMS= 0.1151 Dev= 5.59% S= 71.95 time= 12.20
 Following    2 images are candidates for TS:    7   11  
 Converged to TS (number of iterations):        151
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time=  36.15

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1296 steps. Energy=    -388.0432999       time=       5.30
 Minus side of path:                    1461 steps. Energy=    -388.1198614       time=       5.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0432999  6.1415         -381.9018283  6.2180         -388.1198614  39.379  29.264   2.587  56.050
        *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=    0.14799E+06
 decide> The unconnected minima in the chain and their distances are:
     2       52.03     3     3       19.27     1 
 

 tryconnect> 525-iteration DNEB run for minima 2_F and 3_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 525 RMS= 0.1033 Dev= 5.09% S= 66.81 time= 10.59
 Following    2 images are candidates for TS:    6   11  
 Converged to TS (number of iterations):        103
 Converged to TS (number of iterations):        100
 DNEB run yielded 2 true transition state(s) time=  18.80

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1397 steps. Energy=    -379.0342386       time=       8.02
 Minus side of path:                    1197 steps. Energy=    -382.6739829       time=       4.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.0342386  3.8148         -375.2194456  7.4545         -382.6739829  40.750  35.802   2.284  63.481
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1036 steps. Energy=    -381.8636974       time=       3.63
 Minus side of path:                    1084 steps. Energy=    -387.0586613       time=       3.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.8636974 0.29450         -381.5691967  5.4895         -387.0586613  20.462  18.148   2.552  56.816
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1107 Dev= 0.64% S= 20.76 time= 1.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.62

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     900 steps. Energy=    -392.2659170       time=       2.84
 Minus side of path:                     916 steps. Energy=    -390.6308555       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.2659170  4.4183         -387.8475756  2.7833         -390.6308555  21.376  18.953  14.040  10.328
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     38633.    
 decide> The unconnected minima in the chain and their distances are:
     5       33.74     8     8        5.97     1 
 

 tryconnect> 350-iteration DNEB run for minima 5_F and 8_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5353552375    
 Double-ended search iterations= 350 RMS= 0.1481 Dev= 3.22% S= 40.88 time= 4.98
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   9.54

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     970 steps. Energy=    -384.4448489       time=       2.52
 Minus side of path:                     947 steps. Energy=    -385.0532120       time=       2.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4448489  4.0056         -380.4392870  4.6139         -385.0532120  22.589  17.685  10.054  14.423
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0944 Dev= 0.30% S= 6.01 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   5.91

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     852 steps. Energy=    -391.8645413       time=       2.95
 Minus side of path:                     917 steps. Energy=    -392.2659170       time=       3.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.8645413 0.33217E-01     -391.8313243 0.43459         -392.2659170   6.198   5.971   7.140  20.308
        Known (#1)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     40680.    
 decide> The unconnected minima in the chain and their distances are:
     5       34.39     9 
 

 tryconnect> 350-iteration DNEB run for minima 5_F and 9_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3994903209    
 Double-ended search iterations= 350 RMS= 0.0712 Dev= 1.57% S= 40.09 time= 4.86
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.62

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1519 steps. Energy=    -388.1198614       time=       6.95
 Minus side of path:                    1063 steps. Energy=    -384.4448489       time=       3.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1198614  9.1865         -378.9334043  5.5114         -384.4448489  55.027  46.331   2.842  51.023
        Known (#4)                                              Known (#10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     6501.9    
 decide> The unconnected minima in the chain and their distances are:
     5       18.07    10     3        8.43     9 
 

 tryconnect> 175-iteration DNEB run for minima 5_F and 10_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0864 Dev= 0.31% S= 18.31 time= 1.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   5.74

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     907 steps. Energy=    -382.6739829       time=       2.43
 Minus side of path:                    1053 steps. Energy=    -384.6592017       time=       4.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6739829 0.21385E-01     -382.6525984  2.0066         -384.6592017  17.743  17.437   3.067  47.281
        Known (#5)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1425 Dev= 0.17% S= 8.49 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.76

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     882 steps. Energy=    -388.0432999       time=       3.44
 Minus side of path:                     925 steps. Energy=    -390.6308555       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0432999 0.25051E-01     -388.0182489  2.6126         -390.6308555   8.600   8.429   3.598  40.305
        Known (#3)                                              Known (#9)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     2003.5    
 decide> The unconnected minima in the chain and their distances are:
    12       12.61    10 
 

 tryconnect> 105-iteration DNEB run for minima 10_S and 12_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 2.4156 Dev= 0.92% S= 12.73 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   5.02

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     999 steps. Energy=    -384.6592017       time=       2.76
 Minus side of path:                     927 steps. Energy=    -384.4448489       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6592017  1.1199         -383.5392683 0.90558         -384.4448489  16.168  12.608   2.123  68.310
        Known (#12)                                             Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -391.8645413 0.33217E-01    -391.8313243 0.43459        -392.2659170   6.198   5.971   7.140  20.308
   4     -392.2659170  4.4183        -387.8475756  2.7833        -390.6308555  21.376  18.953  14.040  10.328
   9     -390.6308555  2.6126        -388.0182489 0.25051E-01    -388.0432999   8.600   8.429   3.598  40.305
   1     -388.0432999  6.1415        -381.9018283  6.2180        -388.1198614  39.379  29.264   2.587  56.050
   7     -388.1198614  9.1865        -378.9334043  5.5114        -384.4448489  55.027  46.331   2.842  51.023
  10     -384.4448489 0.90558        -383.5392683  1.1199        -384.6592017  16.168  12.608   2.123  68.310
   8     -384.6592017  2.0066        -382.6525984 0.21385E-01    -382.6739829  17.743  17.437   3.067  47.281
   2     -382.6739829  7.4545        -375.2194456  3.8148        -379.0342386  40.750  35.802   2.284  63.481

 Number of TS in the path       =      8
 Number of cycles               =      6

 Elapsed time=                               208.25
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             59418 time=          79.89 %= 38.4
 OPTIM> # of energy+gradient+Hessian calls=       911 time=           4.62 %=  2.2
