
 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 12:48:47 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=    -389.1566518     RMS force=    0.9922962646E-06
 OPTIM> Final energy  =    -385.4464313     RMS force=    0.8739688527E-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=     708.87    
 decide> The unconnected minima in the chain and their distances are:
     2        8.92     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.7060 Dev= 1.00% S= 9.90 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   5.55

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     923 steps. Energy=    -387.7539719       time=       2.44
 Minus side of path:                     948 steps. Energy=    -389.1566518       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.7539719 0.86433         -386.8896454  2.2670         -389.1566518   5.004   2.825  15.221   9.527
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     566.32    
 decide> The unconnected minima in the chain and their distances are:
     2        8.27     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.7060 Dev= 1.24% S= 9.64 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=   9.70

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1039 steps. Energy=    -388.3145308       time=       3.28
 Minus side of path:                     946 steps. Energy=    -386.0785821       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3145308  2.6695         -385.6450372 0.43354         -386.0785821  29.861  27.441   5.676  25.546
        *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=     366.72    
 decide> The unconnected minima in the chain and their distances are:
     2        4.75     5     5        6.38     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.5482 Dev= 1.13% S= 5.20 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=  11.78

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     978 steps. Energy=    -385.4464313       time=       2.59
 Minus side of path:                    1058 steps. Energy=    -387.6012528       time=       2.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4464313 0.45368         -384.9927513  2.6085         -387.6012528  29.892  27.546   5.559  26.085
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.7449 Dev= 0.24% S= 6.64 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.72

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     944 steps. Energy=    -389.1566518       time=       2.57
 Minus side of path:                     976 steps. Energy=    -386.0785821       time=       2.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1566518  4.5154         -384.6412487  1.4373         -386.0785821  10.270   6.836  24.637   5.886
        Known (#1)                                              Known (#5)
 Unconnected minimum 5 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=     171.28    
 decide> The unconnected minima in the chain and their distances are:
     6        5.55     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.2059 Dev= 1.03% S= 5.96 time= 0.19
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  28.37
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     214.29    
 decide> The unconnected minima in the chain and their distances are:
     2        4.75     5 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 5_S using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 350 RMS= 0.0107 Dev= 4.69% S= 6.73 time= 4.56
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.57

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     939 steps. Energy=    -385.4464313       time=       2.88
 Minus side of path:                     959 steps. Energy=    -386.0785821       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4464313  2.5154         -382.9310619  3.1475         -386.0785821   5.622   4.751  34.992   4.144
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -389.1566518  4.5154        -384.6412487  1.4373        -386.0785821  10.270   6.836  24.637   5.886
   5     -386.0785821  3.1475        -382.9310619  2.5154        -385.4464313   5.622   4.751  34.992   4.144

 Number of TS in the path       =      2
 Number of cycles               =      5

 Elapsed time=                                97.69
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             21865 time=          28.74 %= 29.4
 OPTIM> # of energy+gradient+Hessian calls=       526 time=           2.73 %=  2.8
