
 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)@comp31.ch.
                 Created on  5/28/12 at 13:12:31 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -383.2316760     RMS force=    0.9326983595E-06
 OPTIM> Final energy  =    -391.3156109     RMS force=    0.9142348555E-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=     39462.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.05     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0760 Dev= 1.59% S= 37.80 time= 5.07
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   5.19

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     920 steps. Energy=    -384.8532460       time=       2.98
 Minus side of path:                     961 steps. Energy=    -387.2420025       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8532460 0.20059         -384.6526542  2.5893         -387.2420025   4.497   4.411  15.605   9.292
        *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=     20945.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.81     4     3       19.53     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1135 Dev= 0.59% S= 25.03 time= 2.44
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.88

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     910 steps. Energy=    -388.7676323       time=       2.12
 Minus side of path:                     897 steps. Energy=    -387.2420025       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7676323  1.5507         -387.2168929 0.25110E-01     -387.2420025   6.698   6.060   6.823  21.252
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0658 Dev= 0.13% S= 20.14 time= 1.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.04

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     956 steps. Energy=    -383.2316760       time=       2.37
 Minus side of path:                     926 steps. Energy=    -384.8532460       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.2316760 0.17930         -383.0523749  1.8009         -384.8532460  20.294  19.552   7.523  19.275
        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      4 steps with      1 missing connections, weight=     8357.1    
 decide> The unconnected minima in the chain and their distances are:
     2       20.29     5 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 5_S using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0600 Dev= 0.20% S= 20.75 time= 1.83
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.41

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     941 steps. Energy=    -388.7676323       time=       2.20
 Minus side of path:                     975 steps. Energy=    -389.1057838       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7676323 0.14877         -388.6188614 0.48692         -389.1057838  12.956  12.587   2.013  72.026
        Known (#5)                                              *NEW* (Placed in 6)
 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      5 steps with      1 missing connections, weight=     1358.2    
 decide> The unconnected minima in the chain and their distances are:
     2       11.07     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1040 Dev= 0.10% S= 11.19 time= 0.47
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.30

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     927 steps. Energy=    -389.7215338       time=       2.29
 Minus side of path:                     925 steps. Energy=    -389.1788416       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7215338 0.57132         -389.1502113 0.28630E-01     -389.1788416   2.813   2.787   9.053  16.017
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     1122.1    
 decide> The unconnected minima in the chain and their distances are:
     2       10.38     8     8        1.35     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0812 Dev= 0.15% S= 10.47 time= 0.47
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.58
 isnewts> transition state is the same as number        5 energy=     -389.1502112825
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     930 steps. Energy=    -389.7215338       time=       2.26
 Minus side of path:                     928 steps. Energy=    -389.1788416       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7215338 0.57132         -389.1502113 0.28630E-01     -389.1788416   2.813   2.787   9.052  16.019
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 6_S and 8_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0190 Dev= 0.09% S= 1.35 time= 0.21
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.26

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     920 steps. Energy=    -389.1057838       time=       2.13
 Minus side of path:                     933 steps. Energy=    -389.1788416       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1057838 0.24419E-02     -389.1033419 0.75500E-01     -389.1788416   1.384   1.347   5.237  27.686
        Known (#6)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1171.8    
 decide> The unconnected minima in the chain and their distances are:
     2       10.54     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 3.2544 Dev= 0.08% S= 10.64 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   3.93

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     945 steps. Energy=    -391.3156109       time=       2.26
 Minus side of path:                     929 steps. Energy=    -389.7215338       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.3156109  2.0709         -389.2447121 0.47682         -389.7215338  11.493  10.545   2.010  72.153
        Known (#2)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -383.2316760 0.17930        -383.0523749  1.8009        -384.8532460  20.294  19.552   7.523  19.275
   1     -384.8532460 0.20059        -384.6526542  2.5893        -387.2420025   4.497   4.411  15.605   9.292
   2     -387.2420025 0.25110E-01    -387.2168929  1.5507        -388.7676323   6.698   6.060   6.823  21.252
   4     -388.7676323 0.14877        -388.6188614 0.48692        -389.1057838  12.956  12.587   2.013  72.026
   7     -389.1057838 0.24419E-02    -389.1033419 0.75500E-01    -389.1788416   1.384   1.347   5.237  27.686
   5     -389.1788416 0.28630E-01    -389.1502113 0.57132        -389.7215338   2.813   2.787   9.053  16.017
   8     -389.7215338 0.47682        -389.2447121  2.0709        -391.3156109  11.493  10.545   2.010  72.153

 Number of TS in the path       =      7
 Number of cycles               =      6

 Elapsed time=                                81.47
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             30988 time=          42.33 %= 52.0
 OPTIM> # of energy+gradient+Hessian calls=       250 time=           1.10 %=  1.4
