
 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)@comp27.ch.
                 Created on  5/28/12 at 12:37:10 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=    -389.7161039     RMS force=    0.9875096042E-06
 OPTIM> Final energy  =    -387.5253268     RMS force=    0.8455336978E-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=     2644.6    
 decide> The unconnected minima in the chain and their distances are:
     2       13.83     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2248 Dev= 0.14% S= 14.67 time= 0.71
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.40

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     949 steps. Energy=    -387.5253268       time=       3.04
 Minus side of path:                     984 steps. Energy=    -387.8617245       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5253268 0.44828         -387.0770463 0.78468         -387.8617245   3.638   3.415  12.327  11.763
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2609.8    
 decide> The unconnected minima in the chain and their distances are:
     3       13.77     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2383 Dev= 0.21% S= 14.58 time= 0.73
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        246
 DNEB run yielded 1 true transition state(s) time=  27.23

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     930 steps. Energy=    -386.1410395       time=       2.19
 Minus side of path:                    1210 steps. Energy=    -388.3774993       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1410395 0.51081E-03     -386.1405287  2.2370         -388.3774993  35.784  35.552   2.427  59.747
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     2908.6    
 decide> The unconnected minima in the chain and their distances are:
     3        8.06     5     5       13.36     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0574 Dev= 0.01% S= 8.07 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.39

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     989 steps. Energy=    -387.8617245       time=       3.16
 Minus side of path:                     945 steps. Energy=    -388.3774993       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8617245 0.16890         -387.6928243 0.68468         -388.3774993   8.095   8.060   2.010  72.134
        Known (#3)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1678 Dev= 0.26% S= 14.30 time= 0.72
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.98

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     929 steps. Energy=    -387.8695962       time=       2.26
 Minus side of path:                     943 steps. Energy=    -389.7161039       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8695962  1.7740         -386.0956183  3.6205         -389.7161039   9.973   8.982  27.357   5.300
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     156.96    
 decide> The unconnected minima in the chain and their distances are:
     5        5.39     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2188 Dev= 0.24% S= 5.77 time= 0.18
 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=  31.69
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     313.91    
 decide> The unconnected minima in the chain and their distances are:
     5        5.39     6 
 

 tryconnect> 420-iteration DNEB run for minima 5_F and 6_S using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 420 RMS= 0.2909 Dev= 8.64% S= 9.47 time= 6.34
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.75

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     961 steps. Energy=    -389.7161039       time=       3.12
 Minus side of path:                     956 steps. Energy=    -388.3774993       time=       3.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7161039  5.0907         -384.6253842  3.7521         -388.3774993  14.737  13.376  21.210   6.836
        Known (#1)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -389.7161039  5.0907        -384.6253842  3.7521        -388.3774993  14.737  13.376  21.210   6.836
   3     -388.3774993 0.68468        -387.6928243 0.16890        -387.8617245   8.095   8.060   2.010  72.134
   1     -387.8617245 0.78468        -387.0770463 0.44828        -387.5253268   3.638   3.415  12.327  11.763

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               111.74
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             25335 time=          31.54 %= 28.2
 OPTIM> # of energy+gradient+Hessian calls=       594 time=           3.03 %=  2.7
