
 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)@comp35.ch.
                 Created on  5/28/12 at 12:50:43 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=    -386.0696532     RMS force=    0.9616747486E-06
 OPTIM> Final energy  =    -390.5908303     RMS force=    0.9180623509E-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=     7552.0    
 decide> The unconnected minima in the chain and their distances are:
     2       19.62     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1983 Dev= 0.96% S= 21.45 time= 1.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     947 steps. Energy=    -386.8106153       time=       2.94
 Minus side of path:                     880 steps. Energy=    -386.0696532       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8106153 0.77051         -386.0401015 0.29552E-01     -386.0696532  15.708  15.542   2.957  49.041
        *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=     547.11    
 decide> The unconnected minima in the chain and their distances are:
     2        8.18     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 1.4761 Dev= 0.30% S= 9.84 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.21

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     961 steps. Energy=    -389.8416036       time=       2.96
 Minus side of path:                     938 steps. Energy=    -386.8106153       time=       2.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.8416036  3.6901         -386.1514651 0.65915         -386.8106153   8.807   7.960  28.173   5.147
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1094.2    
 decide> The unconnected minima in the chain and their distances are:
     2        8.18     3 
 

 tryconnect> 630-iteration DNEB run for minima 2_F and 3_S using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 630 RMS= 0.3714 Dev= 3.99% S= 13.82 time= 15.33
 Following    3 images are candidates for TS:    4   10   17  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         20
 Converged to TS (number of iterations):         16
 DNEB run yielded 3 true transition state(s) time=   9.34

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     903 steps. Energy=    -390.5908303       time=       2.06
 Minus side of path:                     888 steps. Energy=    -390.5908303       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5908303  3.8138         -386.7770089  3.8138         -390.5908303   3.599   2.939  48.235   3.006
        Known (#2)                                              Known (#2)
 Alternative path found between members of the F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     932 steps. Energy=    -389.7016758       time=       3.00
 Minus side of path:                     926 steps. Energy=    -389.7016758       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7016758  3.6113         -386.0903989  3.6113         -389.7016758   3.436   2.941  48.245   3.006
        *NEW* (Placed in 5)                                     Known (#5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     959 steps. Energy=    -386.8106153       time=       3.22
 Minus side of path:                     930 steps. Energy=    -386.8106153       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8106153  3.5512         -383.2594178  3.5512         -386.8106153   3.589   2.940  48.215   3.007
        Known (#3)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     460.22    
 decide> The unconnected minima in the chain and their distances are:
     2        7.02     5     5        4.85     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2954 Dev= 0.41% S= 7.43 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   4.20

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     938 steps. Energy=    -390.5908303       time=       3.06
 Minus side of path:                     940 steps. Energy=    -389.7016758       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5908303  3.0495         -387.5413540  2.1603         -389.7016758   7.857   7.022  17.622   8.228
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1503 Dev= 0.32% S= 5.27 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.23

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     948 steps. Energy=    -389.7016758       time=       2.49
 Minus side of path:                     969 steps. Energy=    -386.8106153       time=       2.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7016758  3.7459         -385.9557455 0.85487         -386.8106153   6.340   4.857  41.640   3.482
        Known (#5)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -386.0696532 0.29552E-01    -386.0401015 0.77051        -386.8106153  15.708  15.542   2.957  49.041
   7     -386.8106153 0.85487        -385.9557455  3.7459        -389.7016758   6.340   4.857  41.640   3.482
   6     -389.7016758  2.1603        -387.5413540  3.0495        -390.5908303   7.857   7.022  17.622   8.228
   3     -390.5908303  3.8138        -386.7770089  3.8138        -390.5908303   3.599   2.939  48.235   3.006

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

 Elapsed time=                                81.17
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             32446 time=          42.38 %= 52.2
 OPTIM> # of energy+gradient+Hessian calls=       171 time=           0.78 %=  1.0
