
 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)@comp23.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=    -384.5540878     RMS force=    0.9989892287E-06
 OPTIM> Final energy  =    -380.6460038     RMS force=    0.9329653587E-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=    0.12914E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.55     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0352 Dev= 3.18% S= 58.67 time= 9.46
 Following    2 images are candidates for TS:    7   11  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        157
 Converged to TS (number of iterations):         47
 DNEB run yielded 2 true transition state(s) time=  19.16

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1022 steps. Energy=    -379.3011876       time=       2.50
 Minus side of path:                    1639 steps. Energy=    -384.5540878       time=       7.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.3011876 0.32631         -378.9748767  5.5792         -384.5540878  51.463  46.952   2.012  72.051
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1041 steps. Energy=    -380.6460038       time=       3.46
 Minus side of path:                    1950 steps. Energy=    -382.7382729       time=      11.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.6460038  1.2423         -379.4036991  3.3346         -382.7382729  63.391  56.737   1.783  81.311
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     20953.    
 decide> The unconnected minima in the chain and their distances are:
     4       27.57     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 4_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0557 Dev= 1.31% S= 29.92 time= 3.05
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=   9.13

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     994 steps. Energy=    -384.9821841       time=       2.51
 Minus side of path:                    1013 steps. Energy=    -384.5540878       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.9821841  4.0121         -380.9700522  3.5840         -384.5540878  21.089  18.977   2.522  57.497
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 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=     5417.7    
 decide> The unconnected minima in the chain and their distances are:
     4       17.56     5 
 

 tryconnect> 175-iteration DNEB run for minima 4_F and 5_S using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2893 Dev= 1.87% S= 18.98 time= 1.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.62

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1098 steps. Energy=    -385.3643204       time=       4.07
 Minus side of path:                    1003 steps. Energy=    -382.6403367       time=       2.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.3643204  3.8437         -381.5206440  1.1197         -382.6403367  29.259  25.056   2.185  66.365
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     181.57    
 decide> The unconnected minima in the chain and their distances are:
     4        1.60     7     6        5.62     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 7_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2052 Dev= 0.06% S= 1.60 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.68

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     975 steps. Energy=    -382.7382729       time=       2.18
 Minus side of path:                     976 steps. Energy=    -382.6403367       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.7382729 0.10706         -382.6312132 0.91235E-02     -382.6403367   1.630   1.600   2.126  68.216
        Known (#4)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3441 Dev= 0.97% S= 6.03 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        239
 DNEB run yielded 1 true transition state(s) time=  18.24

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     944 steps. Energy=    -384.6978864       time=       2.14
 Minus side of path:                     996 steps. Energy=    -385.1178926       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6978864 0.66702E-01     -384.6311848 0.48671         -385.1178926  23.344  23.091   2.532  57.262
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     354.95    
 decide> The unconnected minima in the chain and their distances are:
     6        5.62     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 6_F using 12 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0124 Dev= 2.29% S= 8.15 time= 6.30
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.52

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     985 steps. Energy=    -386.0213684       time=       2.24
 Minus side of path:                     947 steps. Energy=    -384.5540878       time=       2.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0213684  3.8566         -382.1647889  2.3893         -384.5540878   8.150   5.735   9.967  14.548
        *NEW* (Placed in 10)                                    Known (#1)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     127.25    
 decide> The unconnected minima in the chain and their distances are:
     6        5.03    10 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 10_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1285 Dev= 0.38% S= 5.09 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.47

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     895 steps. Energy=    -385.3643204       time=       1.90
 Minus side of path:                     977 steps. Energy=    -386.0213684       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.3643204 0.25951E-02     -385.3617253 0.65964         -386.0213684   5.172   5.030   5.529  26.225
        Known (#6)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -384.5540878  2.3893        -382.1647889  3.8566        -386.0213684   8.150   5.735   9.967  14.548
   8     -386.0213684 0.65964        -385.3617253 0.25951E-02    -385.3643204   5.172   5.030   5.529  26.225
   4     -385.3643204  3.8437        -381.5206440  1.1197        -382.6403367  29.259  25.056   2.185  66.365
   5     -382.6403367 0.91235E-02    -382.6312132 0.10706        -382.7382729   1.630   1.600   2.126  68.216
   2     -382.7382729  3.3346        -379.4036991  1.2423        -380.6460038  63.391  56.737   1.783  81.311

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               135.78
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             43118 time=          51.77 %= 38.1
 OPTIM> # of energy+gradient+Hessian calls=       637 time=           2.88 %=  2.1
