
 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 13: 5:41 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=    -381.1278293     RMS force=    0.9343349788E-06
 OPTIM> Final energy  =    -381.9732227     RMS force=    0.9053910381E-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=     18100.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.26     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 245 RMS= 13.4597 Dev= 33.99% S= 34.41 time= 1.98
 Following    2 images are candidates for TS:    2    4  
 Converged to TS (number of iterations):        156
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=  48.66

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1039 steps. Energy=    -381.1466521       time=       3.03
 Minus side of path:                    1020 steps. Energy=    -381.1278293       time=       3.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1466521 0.42408         -380.7225717 0.40526         -381.1278293  30.808  28.622   1.893  76.599
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     990 steps. Energy=    -381.1278293       time=       4.28
 Minus side of path:                    1005 steps. Energy=    -381.8381065       time=       5.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1278293  2.4713         -378.6565693  3.1815         -381.8381065   6.314   5.526  31.538   4.598
        Known (#1)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     859.88    
 decide> The unconnected minima in the chain and their distances are:
     2        9.51     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 113 RMS= 4.6700 Dev= 15.23% S= 10.21 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   7.04

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1011 steps. Energy=    -381.9732227       time=       3.79
 Minus side of path:                    1020 steps. Energy=    -381.8539567       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.9732227 0.85101         -381.1222176 0.73174         -381.8539567   7.433   7.292   5.908  24.545
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     182.50    
 decide> The unconnected minima in the chain and their distances are:
     5        5.67     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.2190 Dev= 1.02% S= 6.07 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   8.81
 isnewts> transition state is the same as number        1 energy=     -380.7225717432
 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:                    1052 steps. Energy=    -381.1466521       time=       2.48
 Minus side of path:                    1014 steps. Energy=    -381.1278293       time=       2.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1466521 0.42408         -380.7225717 0.40526         -381.1278293  30.808  28.624   1.893  76.582
        Known (#3)                                              Known (#1)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     365.01    
 decide> The unconnected minima in the chain and their distances are:
     5        5.67     3 
 

 tryconnect> 455-iteration DNEB run for minima 3_S and 5_F using 13 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 455 RMS= 0.0327 Dev= 4.00% S= 7.88 time= 6.69
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   4.19

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1018 steps. Energy=    -381.1466521       time=       3.82
 Minus side of path:                    1005 steps. Energy=    -381.8539567       time=       3.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1466521  2.4721         -378.6745126  3.1794         -381.8539567   6.431   5.673  32.751   4.427
        Known (#3)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -381.1278293 0.40526        -380.7225717 0.42408        -381.1466521  30.808  28.622   1.893  76.599
   5     -381.1466521  2.4721        -378.6745126  3.1794        -381.8539567   6.431   5.673  32.751   4.427
   3     -381.8539567 0.73174        -381.1222176 0.85101        -381.9732227   7.433   7.292   5.908  24.545

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

 Elapsed time=                               112.24
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             26473 time=          29.80 %= 26.6
 OPTIM> # of energy+gradient+Hessian calls=       344 time=           1.52 %=  1.4
