
 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 12:59: 7 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=    -388.1160328     RMS force=    0.9368442178E-06
 OPTIM> Final energy  =    -387.4135552     RMS force=    0.8265137008E-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=     17562.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.99     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 245 RMS= 0.1285 Dev= 1.34% S= 28.23 time= 2.38
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   6.65

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1044 steps. Energy=    -388.1071294       time=       3.74
 Minus side of path:                     902 steps. Energy=    -385.9146793       time=       3.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1071294  2.3535         -385.7536522 0.16103         -385.9146793  14.606  13.301   9.546  15.190
        *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      3 steps with      2 missing connections, weight=     5510.6    
 decide> The unconnected minima in the chain and their distances are:
     2       13.43     3     4       14.56     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 140 RMS= 0.0800 Dev= 0.10% S= 13.64 time= 0.80
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=   8.22

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     961 steps. Energy=    -387.9306687       time=       3.33
 Minus side of path:                    1063 steps. Energy=    -387.4135552       time=       3.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9306687  1.0530         -386.8776720 0.53588         -387.4135552  26.623  25.018   2.606  55.645
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.1546 Dev= 0.69% S= 15.22 time= 0.77
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   5.43

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     870 steps. Energy=    -385.9146793       time=       2.74
 Minus side of path:                     970 steps. Energy=    -386.8959175       time=       3.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9146793 0.71736E-01     -385.8429433  1.0530         -386.8959175  14.216  13.834   4.033  35.953
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     2868.2    
 decide> The unconnected minima in the chain and their distances are:
     5       14.00     6     6        4.99     1 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.3192 Dev= 1.15% S= 14.33 time= 0.78
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        137
 DNEB run yielded 1 true transition state(s) time=  19.51
 isnewts> transition state is the same as number        2 energy=     -386.8776719723
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1089 steps. Energy=    -387.4135552       time=       3.37
 Minus side of path:                     935 steps. Energy=    -387.9306687       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4135552 0.53588         -386.8776720  1.0530         -387.9306687  26.623  25.018   2.604  55.680
        Known (#2)                                              Known (#5)
 Alternative path found between members of the F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.3215 Dev= 1.69% S= 5.46 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   7.50

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     912 steps. Energy=    -386.8959175       time=       3.26
 Minus side of path:                     937 steps. Energy=    -387.9306687       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8959175 0.86114         -386.0347803  1.8959         -387.9306687  16.073  14.008   3.984  36.398
        Known (#6)                                              Known (#5)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     248.93    
 decide> The unconnected minima in the chain and their distances are:
     6        4.99     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 6_F using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0099 Dev= 2.03% S= 7.19 time= 5.81
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   4.10

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     924 steps. Energy=    -388.1160328       time=       3.80
 Minus side of path:                     912 steps. Energy=    -386.8959175       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1160328  3.5143         -384.6017369  2.2942         -386.8959175   5.796   4.994  38.589   3.758
        Known (#1)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -388.1160328  3.5143        -384.6017369  2.2942        -386.8959175   5.796   4.994  38.589   3.758
   5     -386.8959175 0.86114        -386.0347803  1.8959        -387.9306687  16.073  14.008   3.984  36.398
   2     -387.9306687  1.0530        -386.8776720 0.53588        -387.4135552  26.623  25.018   2.606  55.645

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                               100.85
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             26152 time=          35.85 %= 35.6
 OPTIM> # of energy+gradient+Hessian calls=       460 time=           2.30 %=  2.3
