
 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)@comp34.ch.
                 Created on  5/28/12 at 13: 2:33 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=    -378.2543928     RMS force=    0.9482239899E-06
 OPTIM> Final energy  =    -381.5005310     RMS force=    0.9287468886E-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=    0.11864E+06
 decide> The unconnected minima in the chain and their distances are:
     2       49.14     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3623494974    
 Double-ended search iterations= 490 RMS= 0.0754 Dev= 1.60% S= 58.40 time= 7.48
 Following    2 images are candidates for TS:    6   11  
 Converged to TS (number of iterations):        100
 Converged to TS (number of iterations):         37
 DNEB run yielded 2 true transition state(s) time=  15.51

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1189 steps. Energy=    -380.1934631       time=       4.75
 Minus side of path:                    1133 steps. Energy=    -378.2462887       time=       4.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631  5.1580         -375.0355024  3.2108         -378.2462887  49.203  38.313   2.842  51.019
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1010 steps. Energy=    -379.5013770       time=       3.62
 Minus side of path:                    1012 steps. Energy=    -379.7128734       time=       3.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.5013770 0.33242         -379.1689612 0.54391         -379.7128734   7.877   7.820   1.726  84.033
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     5524.7    
 decide> The unconnected minima in the chain and their distances are:
     2       17.67     3     4        2.09     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 2.7344 Dev= 0.50% S= 18.48 time= 1.04
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   5.94

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1023 steps. Energy=    -381.8415109       time=       4.77
 Minus side of path:                    1021 steps. Energy=    -380.1934631       time=       2.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.8415109  2.5672         -379.2743536 0.91911         -380.1934631  19.523  17.965   3.059  47.399
        *NEW* (Placed in 7)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0176 Dev= 0.91% S= 2.09 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.23

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1009 steps. Energy=    -378.2543928       time=       2.34
 Minus side of path:                    1005 steps. Energy=    -378.2462887       time=       2.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.2543928 0.56854E-01     -378.1975387 0.48750E-01     -378.2462887   2.221   2.088   9.845  14.729
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     789.04    
 decide> The unconnected minima in the chain and their distances are:
     2        9.24     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2260 Dev= 0.65% S= 9.49 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        101
 DNEB run yielded 1 true transition state(s) time=   7.86

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1167 steps. Energy=    -386.0055417       time=       3.67
 Minus side of path:                    1020 steps. Energy=    -381.5005310       time=       2.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0055417  4.9567         -381.0487972 0.45173         -381.5005310  23.337  19.925   2.514  57.666
        *NEW* (Placed in 8)                                     Known (#2)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1578.1    
 decide> The unconnected minima in the chain and their distances are:
     2        9.24     7 
 

 tryconnect> 735-iteration DNEB run for minima 2_F and 7_S using 21 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1675721423E-01
 Double-ended search iterations= 735 RMS= 0.0046 Dev= 3.36% S= 13.37 time= 17.59
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.75

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1024 steps. Energy=    -381.8415109       time=       2.71
 Minus side of path:                     997 steps. Energy=    -381.5005310       time=       2.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.8415109  2.3817         -379.4597675  2.0408         -381.5005310  11.466   9.244   7.138  20.313
        Known (#7)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -378.2543928 0.56854E-01    -378.1975387 0.48750E-01    -378.2462887   2.221   2.088   9.845  14.729
   1     -378.2462887  3.2108        -375.0355024  5.1580        -380.1934631  49.203  38.313   2.842  51.019
   3     -380.1934631 0.91911        -379.2743536  2.5672        -381.8415109  19.523  17.965   3.059  47.399
   6     -381.8415109  2.3817        -379.4597675  2.0408        -381.5005310  11.466   9.244   7.138  20.313

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

 Elapsed time=                               103.83
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             42285 time=          45.74 %= 44.1
 OPTIM> # of energy+gradient+Hessian calls=       306 time=           1.43 %=  1.4
