
 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: 5:59 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=    -385.8079668     RMS force=    0.9722541170E-06
 OPTIM> Final energy  =    -385.2626841     RMS force=    0.9578389499E-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=     1067.2    
 decide> The unconnected minima in the chain and their distances are:
     2       10.22     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 105 RMS= 1.1431 Dev= 2.14% S= 10.76 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.46

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     971 steps. Energy=    -385.0282936       time=       2.78
 Minus side of path:                    1024 steps. Energy=    -386.2874961       time=       3.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0282936 0.93007         -384.0982217  2.1893         -386.2874961   9.016   8.161   1.879  77.149
        *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      2 steps with      2 missing connections, weight=     823.98    
 decide> The unconnected minima in the chain and their distances are:
     2        4.61     3     3        8.99     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 1.0030 Dev= 0.78% S= 4.92 time= 0.16
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        124
 DNEB run yielded 1 true transition state(s) time=  12.02

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     986 steps. Energy=    -385.0282936       time=       2.38
 Minus side of path:                    1016 steps. Energy=    -387.0122114       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0282936 0.73824         -384.2900510  2.7222         -387.0122114  24.204  23.846   2.531  57.292
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.4031 Dev= 0.12% S= 9.11 time= 0.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.97
 isnewts> transition state is the same as number        1 energy=     -384.0982217192
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1020 steps. Energy=    -386.2874961       time=       3.17
 Minus side of path:                     991 steps. Energy=    -385.0282936       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2874961  2.1893         -384.0982217 0.93007         -385.0282936   9.016   8.161   1.879  77.150
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     1147.7    
 decide> The unconnected minima in the chain and their distances are:
     2        5.12     4     4       10.04     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      16.28894627    
 Double-ended search iterations= 70 RMS= 0.9256 Dev= 2.41% S= 5.50 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   4.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     997 steps. Energy=    -385.2626841       time=       3.45
 Minus side of path:                    1014 steps. Energy=    -387.1186528       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2626841  3.0146         -382.2480505  4.8706         -387.1186528  12.088   4.668   3.230  44.898
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      22.92018318    
 Double-ended search iterations= 105 RMS= 0.3079 Dev= 0.58% S= 10.07 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.95

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1010 steps. Energy=    -386.2874961       time=       3.29
 Minus side of path:                     984 steps. Energy=    -385.8079668       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2874961 0.70279         -385.5847088 0.22326         -385.8079668  10.925  10.046   1.633  88.819
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     195.79    
 decide> The unconnected minima in the chain and their distances are:
     6        5.81     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.1274 Dev= 0.29% S= 5.82 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.03

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     997 steps. Energy=    -386.2874961       time=       2.14
 Minus side of path:                     997 steps. Energy=    -387.1186528       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2874961 0.12934         -386.1581563 0.96050         -387.1186528   6.020   5.807   2.047  70.846
        Known (#4)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -385.8079668 0.22326        -385.5847088 0.70279        -386.2874961  10.925  10.046   1.633  88.819
   6     -386.2874961 0.12934        -386.1581563 0.96050        -387.1186528   6.020   5.807   2.047  70.846
   4     -387.1186528  4.8706        -382.2480505  3.0146        -385.2626841  12.088   4.668   3.230  44.898

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

 Elapsed time=                                68.58
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             19622 time=          21.36 %= 31.1
 OPTIM> # of energy+gradient+Hessian calls=       227 time=           1.11 %=  1.6
