
 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)@comp23.ch.
                 Created on  5/28/12 at 13: 7:59 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>> 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)  ...
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 560 RMS= 0.1056 Dev= 7.26% S= 77.08 time= 12.14
 Following    3 images are candidates for TS:    5    7   12  
 Converged to TS (number of iterations):        222
 Converged to TS (number of iterations):        114
 Converged to TS (number of iterations):        102
 DNEB run yielded 3 true transition state(s) time=  39.27

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     934 steps. Energy=    -387.9522305       time=       3.04
 Minus side of path:                     967 steps. Energy=    -391.8645413       time=       2.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9522305 0.14843         -387.8038039  4.0607         -391.8645413  14.758  13.571   2.638  54.974
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1214 steps. Energy=    -382.1830963       time=       3.90
 Minus side of path:                    1032 steps. Energy=    -380.3293306       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1830963  3.1628         -379.0203160  1.3090         -380.3293306  35.914  28.849   2.699  53.723
        *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:                    1201 steps. Energy=    -382.6739829       time=       3.57
 Minus side of path:                    1327 steps. Energy=    -379.0342386       time=       4.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6739829  7.4545         -375.2194456  3.8148         -379.0342386  40.750  35.802   2.285  63.466
        *NEW* (Placed in 6)                                     Known (#2)
 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)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0969 Dev= 3.16% S= 41.69 time= 4.89
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        154
 DNEB run yielded 1 true transition state(s) time=  11.72

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     924 steps. Energy=    -382.6739829       time=       2.47
 Minus side of path:                    1055 steps. Energy=    -384.6592017       time=       4.02

         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   3.066  47.285
        Known (#6)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     44472.    
 decide> The unconnected minima in the chain and their distances are:
     6       35.43     3 
 

 tryconnect> 350-iteration DNEB run for minima 3_S and 6_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0950 Dev= 2.69% S= 42.26 time= 4.95
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   7.50

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     964 steps. Energy=    -384.4448489       time=       2.88
 Minus side of path:                     948 steps. Energy=    -385.0532120       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4448489  4.0056         -380.4392870  4.6139         -385.0532120  22.589  17.686  10.050  14.428
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     49379.    
 decide> The unconnected minima in the chain and their distances are:
     7       12.61     8     9       36.18     1 
 

 tryconnect> 105-iteration DNEB run for minima 7_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5269 Dev= 0.23% S= 12.71 time= 0.49
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.87

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     932 steps. Energy=    -384.4448489       time=       2.30
 Minus side of path:                     995 steps. Energy=    -384.6592017       time=       2.68

         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   2.123  68.309
        Known (#8)                                              Known (#7)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 9_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1127 Dev= 3.32% S= 41.92 time= 4.97
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   5.68

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1127 steps. Energy=    -385.0532120       time=       3.23
 Minus side of path:                    1135 steps. Energy=    -387.7639469       time=       3.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0532120  3.0541         -381.9990803  5.7649         -387.7639469  34.347  29.257   2.756  52.621
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     7269.7    
 decide> The unconnected minima in the chain and their distances are:
    10       19.37     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 10_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0520 Dev= 0.10% S= 19.73 time= 1.33
 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=  20.59
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     10277.    
 decide> The unconnected minima in the chain and their distances are:
    10       21.74     3 
 

 tryconnect> 210-iteration DNEB run for minima 3_S and 10_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1103 Dev= 1.18% S= 22.83 time= 1.85
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   6.47
 isnewts> transition state is the same as number        1 energy=     -387.8038039456
 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:                     935 steps. Energy=    -387.9522305       time=       2.63
 Minus side of path:                     983 steps. Energy=    -391.8645413       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9522305 0.14843         -387.8038039  4.0607         -391.8645413  14.758  13.571   2.636  55.012
        Known (#3)                                              Known (#1)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     14539.    
 decide> The unconnected minima in the chain and their distances are:
    10       19.37     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 10_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.5098621309    
 Double-ended search iterations= 805 RMS= 0.0283 Dev= 5.12% S= 23.45 time= 26.01
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.25

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1047 steps. Energy=    -391.8645413       time=       4.92
 Minus side of path:                     964 steps. Energy=    -387.7639469       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.8645413  4.3497         -387.5148117 0.24914         -387.7639469  21.948  19.372   3.832  37.838
        Known (#1)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -391.8645413  4.3497        -387.5148117 0.24914        -387.7639469  21.948  19.372   3.832  37.838
   7     -387.7639469  5.7649        -381.9990803  3.0541        -385.0532120  34.347  29.257   2.756  52.621
   5     -385.0532120  4.6139        -380.4392870  4.0056        -384.4448489  22.589  17.686  10.050  14.428
   6     -384.4448489 0.90558        -383.5392683  1.1199        -384.6592017  16.168  12.608   2.123  68.309
   4     -384.6592017  2.0066        -382.6525984 0.21385E-01    -382.6739829  17.743  17.437   3.066  47.285
   3     -382.6739829  7.4545        -375.2194456  3.8148        -379.0342386  40.750  35.802   2.285  63.466

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               213.49
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             70711 time=          95.15 %= 44.6
 OPTIM> # of energy+gradient+Hessian calls=      1057 time=           5.39 %=  2.5
