
 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 13:13:21 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=    -376.9945254     RMS force=    0.9830761363E-06
 OPTIM> Final energy  =    -378.5561821     RMS force=    0.8898452773E-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=     2835.7    
 decide> The unconnected minima in the chain and their distances are:
     2       14.15     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.8060 Dev= 0.67% S= 18.26 time= 0.63
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   5.33

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1014 steps. Energy=    -377.9127493       time=       3.90
 Minus side of path:                    1004 steps. Energy=    -376.9945254       time=       3.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.9127493  2.9448         -374.9679755  2.0265         -376.9945254   6.680   5.823  24.592   5.896
        *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=     2395.5    
 decide> The unconnected minima in the chain and their distances are:
     2       13.38     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_S using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.4110 Dev= 0.63% S= 17.55 time= 0.67
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        208
 DNEB run yielded 1 true transition state(s) time=  24.15

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1016 steps. Energy=    -379.1634843       time=       3.19
 Minus side of path:                     996 steps. Energy=    -379.1718840       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.1634843 0.48654E-01     -379.1148308 0.57053E-01     -379.1718840   2.200   2.068  10.206  14.208
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1643.8    
 decide> The unconnected minima in the chain and their distances are:
     2        7.90     4     4       10.48     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2149 Dev= 0.47% S= 8.22 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        171
 DNEB run yielded 1 true transition state(s) time=  13.18

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1107 steps. Energy=    -378.1292048       time=       2.62
 Minus side of path:                    1076 steps. Energy=    -378.5561821       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.1292048 0.77893         -377.3502753  1.2059         -378.5561821  40.452  35.395   1.807  80.254
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 4_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3369 Dev= 0.59% S= 14.52 time= 0.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.39

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1051 steps. Energy=    -377.9127493       time=       2.32
 Minus side of path:                    1047 steps. Energy=    -379.1634843       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.9127493  3.1548         -374.7579772  4.4055         -379.1634843  18.174  10.499  17.519   8.277
        Known (#3)                                              Known (#4)
 Unconnected minimum 4 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=     519.17    
 decide> The unconnected minima in the chain and their distances are:
     2        8.04     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4708 Dev= 0.45% S= 8.35 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   3.72

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1020 steps. Energy=    -378.5561821       time=       2.22
 Minus side of path:                    1010 steps. Energy=    -378.5567904       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.5561821 0.52828E-01     -378.5033545 0.53436E-01     -378.5567904   2.243   2.105  10.151  14.285
        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      5 steps with      1 missing connections, weight=     497.61    
 decide> The unconnected minima in the chain and their distances are:
     7        7.92     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 7_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2410 Dev= 0.38% S= 8.24 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        131
 DNEB run yielded 1 true transition state(s) time=   9.08

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1139 steps. Energy=    -378.5567904       time=       2.75
 Minus side of path:                     981 steps. Energy=    -377.4544108       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.5567904  1.2447         -377.3121213 0.14229         -377.4544108  30.901  30.012   3.006  48.240
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     577.20    
 decide> The unconnected minima in the chain and their distances are:
     7        8.33     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 7_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7170 Dev= 0.39% S= 8.65 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.00
 isnewts> transition state is the same as number        5 energy=     -378.5033544989
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1013 steps. Energy=    -378.5561821       time=       2.18
 Minus side of path:                    1004 steps. Energy=    -378.5567904       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.5561821 0.52828E-01     -378.5033545 0.53436E-01     -378.5567904   2.243   2.105  10.150  14.285
        Known (#2)                                              Known (#7)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     986.54    
 decide> The unconnected minima in the chain and their distances are:
     2        7.90     4 
 

 tryconnect> 630-iteration DNEB run for minima 2_F and 4_S using 18 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1238691290    
 Double-ended search iterations= 630 RMS= 0.0169 Dev= 4.55% S= 11.35 time= 11.87
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.72

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1004 steps. Energy=    -379.1634843       time=       2.16
 Minus side of path:                    1006 steps. Energy=    -378.5561821       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.1634843  2.9533         -376.2102328  2.3459         -378.5561821   9.295   7.905  17.705   8.190
        Known (#4)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -376.9945254  2.0265        -374.9679755  2.9448        -377.9127493   6.680   5.823  24.592   5.896
   4     -377.9127493  3.1548        -374.7579772  4.4055        -379.1634843  18.174  10.499  17.519   8.277
   8     -379.1634843  2.9533        -376.2102328  2.3459        -378.5561821   9.295   7.905  17.705   8.190

 Number of TS in the path       =      3
 Number of cycles               =      7

 Elapsed time=                               122.10
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             39642 time=          41.08 %= 33.6
 OPTIM> # of energy+gradient+Hessian calls=       668 time=           2.81 %=  2.3
