
 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)@comp25.ch.
                 Created on  5/28/12 at 12:48:28 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=    -385.3808385     RMS force=    0.8077090704E-06
 OPTIM> Final energy  =    -388.1220531     RMS force=    0.9615613714E-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=     18404.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.40     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 245 RMS= 0.2175 Dev= 1.32% S= 28.28 time= 2.03
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):         56
 Converged to TS (number of iterations):        244
 DNEB run yielded 2 true transition state(s) time=  32.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1654 steps. Energy=    -388.6037785       time=       6.60
 Minus side of path:                    1010 steps. Energy=    -385.5138985       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6037785  4.8730         -383.7308206  1.7831         -385.5138985  35.997  26.976   2.082  69.648
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1059 steps. Energy=    -387.9785609       time=       2.75
 Minus side of path:                    1082 steps. Energy=    -388.1121618       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9785609 0.42099E-01     -387.9364618 0.17570         -388.1121618  18.859  18.435   2.466  58.799
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     178.33    
 decide> The unconnected minima in the chain and their distances are:
     2        5.22     3     4        3.29     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.2732 Dev= 1.33% S= 5.65 time= 0.17
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  26.63

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0957 Dev= 0.48% S= 3.31 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   4.38

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     986 steps. Energy=    -385.5138985       time=       3.45
 Minus side of path:                     995 steps. Energy=    -385.3808385       time=       2.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5138985 0.18241         -385.3314907 0.49348E-01     -385.3808385   3.329   3.293  11.042  13.132
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     203.70    
 decide> The unconnected minima in the chain and their distances are:
     2        2.25     6     6        5.77     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0214 Dev= 0.12% S= 2.26 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.34

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     968 steps. Energy=    -388.1220531       time=       2.30
 Minus side of path:                     944 steps. Energy=    -388.1121618       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1220531 0.64365E-01     -388.0576878 0.54474E-01     -388.1121618   2.271   2.254   6.758  21.457
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.4492 Dev= 0.03% S= 6.17 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   4.32
 isnewts> transition state is the same as number        4 energy=     -388.0576877661
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     955 steps. Energy=    -388.1220531       time=       2.56
 Minus side of path:                     974 steps. Energy=    -388.1121618       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1220531 0.64365E-01     -388.0576878 0.54474E-01     -388.1121618   2.271   2.254   6.758  21.456
        Known (#2)                                              Known (#6)
 Alternative path found between members of the 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=     285.28    
 decide> The unconnected minima in the chain and their distances are:
     2        5.22     3 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 3_S using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0090 Dev= 2.16% S= 7.40 time= 6.29
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     994 steps. Energy=    -388.1220531       time=       4.14
 Minus side of path:                     997 steps. Energy=    -388.6037785       time=       2.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1220531  2.5952         -385.5268712  3.0769         -388.6037785   5.936   5.226  35.087   4.133
        Known (#2)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -385.3808385 0.49348E-01    -385.3314907 0.18241        -385.5138985   3.329   3.293  11.042  13.132
   1     -385.5138985  1.7831        -383.7308206  4.8730        -388.6037785  35.997  26.976   2.082  69.648
   6     -388.6037785  3.0769        -385.5268712  2.5952        -388.1220531   5.936   5.226  35.087   4.133

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

 Elapsed time=                               122.30
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             29265 time=          35.27 %= 28.8
 OPTIM> # of energy+gradient+Hessian calls=       619 time=           2.99 %=  2.4
