
 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)@comp20.ch.
                 Created on  5/28/12 at 13: 5:27 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=    -382.2945320     RMS force=    0.9711961287E-06
 OPTIM> Final energy  =    -378.3909776     RMS force=    0.7549428702E-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=     45608.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.73     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      52.53347969    
 Double-ended search iterations= 350 RMS= 1.5961 Dev= 0.40% S= 37.05 time= 3.97
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):         91
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time=  29.81

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1272 steps. Energy=    -384.1799149       time=       3.59
 Minus side of path:                    1065 steps. Energy=    -379.5013770       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1799149  5.3242         -378.8556778 0.64570         -379.5013770  29.913  19.275   2.761  52.525
        *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      3 steps with      2 missing connections, weight=     5032.9    
 decide> The unconnected minima in the chain and their distances are:
     2       12.86     4     3       14.27     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      18.85649142    
 Double-ended search iterations= 105 RMS= 1.1885 Dev= 3.74% S= 13.17 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   5.45

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1134 steps. Energy=    -384.1799149       time=       5.02
 Minus side of path:                    1279 steps. Energy=    -378.3924886       time=       6.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1799149  7.1557         -377.0242383  1.3683         -378.3924886  37.574  34.453   2.072  69.993
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 140 RMS= 0.3786 Dev= 2.11% S= 14.63 time= 0.67
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   6.91

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1044 steps. Energy=    -382.2945320       time=       4.43
 Minus side of path:                    1014 steps. Energy=    -384.1799149       time=       3.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.2945320  4.0083         -378.2861827  5.8937         -384.1799149  20.280  14.295   2.318  62.555
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4249.0    
 decide> The unconnected minima in the chain and their distances are:
     2       12.86     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 805 RMS= 0.0224 Dev= 5.99% S= 18.24 time= 20.20
 Following    2 images are candidates for TS:    7   17  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=  21.51

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1024 steps. Energy=    -379.7128734       time=       2.23
 Minus side of path:                    1004 steps. Energy=    -379.5013770       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.7128734 0.54391         -379.1689612 0.33242         -379.5013770   7.877   7.820   1.726  84.032
        *NEW* (Placed in 6)                                     Known (#4)
 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=     1530.3    
 decide> The unconnected minima in the chain and their distances are:
     2       11.52     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      22.92018318    
 Double-ended search iterations= 105 RMS= 0.9223 Dev= 3.12% S= 11.91 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.28

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1058 steps. Energy=    -378.3909776       time=       2.35
 Minus side of path:                    1098 steps. Energy=    -383.7903472       time=       2.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.3909776  1.2412         -377.1497735  6.6406         -383.7903472  28.736  26.648   2.550  56.867
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1179.9    
 decide> The unconnected minima in the chain and their distances are:
     7       10.57     3 
 

 tryconnect> 105-iteration DNEB run for minima 3_S and 7_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      15.51328216    
 Double-ended search iterations= 105 RMS= 0.2468 Dev= 0.55% S= 10.60 time= 0.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.00

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1022 steps. Energy=    -384.1799149       time=       2.21
 Minus side of path:                     990 steps. Energy=    -383.7903472       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1799149 0.88888         -383.2910326 0.49931         -383.7903472  11.985  10.577   1.506  96.297
        Known (#3)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -382.2945320  4.0083        -378.2861827  5.8937        -384.1799149  20.280  14.295   2.318  62.555
   6     -384.1799149 0.88888        -383.2910326 0.49931        -383.7903472  11.985  10.577   1.506  96.297
   5     -383.7903472  6.6406        -377.1497735  1.2412        -378.3909776  28.736  26.648   2.550  56.867

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

 Elapsed time=                               136.72
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             46324 time=          49.28 %= 36.0
 OPTIM> # of energy+gradient+Hessian calls=       745 time=           3.38 %=  2.5
