
 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)@comp19.ch.
                 Created on  5/28/12 at 13:11:37 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 560 RMS= 0.1903 Dev= 6.13% S= 74.27 time= 12.15
 Following    3 images are candidates for TS:    5    7   12  
 Converged to TS (number of iterations):        208
 Converged to TS (number of iterations):        142
 Converged to TS (number of iterations):         90
 DNEB run yielded 3 true transition state(s) time=  36.44

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     933 steps. Energy=    -391.8645413       time=       2.87
 Minus side of path:                    1039 steps. Energy=    -394.1682877       time=       3.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.8645413 0.54068         -391.3238644  2.8444         -394.1682877  19.752  18.319   2.210  65.615
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1283 steps. Energy=    -388.0432999       time=       5.44
 Minus side of path:                    1462 steps. Energy=    -388.1198614       time=       7.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0432999  6.1415         -381.9018283  6.2180         -388.1198614  39.377  29.265   2.582  56.156
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1391 steps. Energy=    -379.0342386       time=       5.91
 Minus side of path:                    1198 steps. Energy=    -382.6739829       time=       5.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.0342386  3.8148         -375.2194456  7.4545         -382.6739829  40.749  35.801   2.282  63.535
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     43039.    
 decide> The unconnected minima in the chain and their distances are:
     6       35.04     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 6_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7909635100    
 Double-ended search iterations= 350 RMS= 0.1690 Dev= 3.62% S= 39.94 time= 4.92
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   7.97

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     955 steps. Energy=    -385.0532120       time=       3.78
 Minus side of path:                     943 steps. Energy=    -384.4448489       time=       2.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0532120  4.6139         -380.4392870  4.0056         -384.4448489  22.589  17.686  10.044  14.437
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     49611.    
 decide> The unconnected minima in the chain and their distances are:
     6       34.89     4     4       19.27     1 
 

 tryconnect> 350-iteration DNEB run for minima 4_U and 6_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.2088 Dev= 1.50% S= 40.34 time= 4.90
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   6.49

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1524 steps. Energy=    -388.1198614       time=       9.05
 Minus side of path:                    1077 steps. Energy=    -384.4448489       time=       3.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1198614  9.1865         -378.9334043  5.5114         -384.4448489  55.022  46.329   2.846  50.950
        Known (#5)                                              Known (#8)
 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 #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.4027 Dev= 0.63% S= 20.88 time= 1.26
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.41

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     928 steps. Energy=    -390.6308555       time=       3.19
 Minus side of path:                     919 steps. Energy=    -392.2659170       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.6308555  2.7833         -387.8475756  4.4183         -392.2659170  21.376  18.953  14.038  10.329
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      3 missing connections, weight=     6714.8    
 decide> The unconnected minima in the chain and their distances are:
     6       18.07     8     4        8.43     9    10        5.97     1 
 

 tryconnect> 175-iteration DNEB run for minima 6_F and 8_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 175 RMS= 0.3969 Dev= 0.23% S= 18.28 time= 1.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   5.90

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     909 steps. Energy=    -382.6739829       time=       2.80
 Minus side of path:                    1068 steps. Energy=    -384.6592017       time=       3.46

         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   3.068  47.268
        Known (#6)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 9_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1111 Dev= 0.57% S= 8.49 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   4.12

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     896 steps. Energy=    -388.0432999       time=       2.84
 Minus side of path:                     934 steps. Energy=    -390.6308555       time=       2.16

         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   3.597  40.309
        Known (#4)                                              Known (#9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 10_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0623 Dev= 0.39% S= 6.01 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   3.89

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     852 steps. Energy=    -391.8645413       time=       1.92
 Minus side of path:                     906 steps. Energy=    -392.2659170       time=       2.10

         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   7.141  20.306
        Known (#1)                                              Known (#10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 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:
    11       12.61     8 
 

 tryconnect> 105-iteration DNEB run for minima 8_S and 11_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1156 Dev= 0.36% S= 12.71 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=   3.50

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     941 steps. Energy=    -384.4448489       time=       2.23
 Minus side of path:                     998 steps. Energy=    -384.6592017       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4448489 0.90558         -383.5392683  1.1199         -384.6592017  16.168  12.608   2.122  68.316
        Known (#8)                                              Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -391.8645413 0.33217E-01    -391.8313243 0.43459        -392.2659170   6.198   5.971   7.141  20.306
   6     -392.2659170  4.4183        -387.8475756  2.7833        -390.6308555  21.376  18.953  14.038  10.329
   8     -390.6308555  2.6126        -388.0182489 0.25051E-01    -388.0432999   8.600   8.429   3.597  40.309
   2     -388.0432999  6.1415        -381.9018283  6.2180        -388.1198614  39.377  29.265   2.582  56.156
   5     -388.1198614  9.1865        -378.9334043  5.5114        -384.4448489  55.022  46.329   2.846  50.950
  10     -384.4448489 0.90558        -383.5392683  1.1199        -384.6592017  16.168  12.608   2.122  68.316
   7     -384.6592017  2.0066        -382.6525984 0.21385E-01    -382.6739829  17.743  17.437   3.068  47.268
   3     -382.6739829  7.4545        -375.2194456  3.8148        -379.0342386  40.749  35.801   2.282  63.535

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                               172.14
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             50423 time=          68.24 %= 39.6
 OPTIM> # of energy+gradient+Hessian calls=       736 time=           3.46 %=  2.0
