
 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: 6:17 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=    -392.1126712     RMS force=    0.9748240394E-06
 OPTIM> Final energy  =    -392.6563397     RMS force=    0.9925367704E-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=     1044.7    
 decide> The unconnected minima in the chain and their distances are:
     2       10.15     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0605 Dev= 0.12% S= 10.22 time= 0.46
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   5.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1127 steps. Energy=    -392.5861740       time=       3.06
 Minus side of path:                     947 steps. Energy=    -392.3677491       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.5861740 0.39670         -392.1894696 0.17828         -392.3677491  10.056   9.154   3.990  36.344
        *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=     125.39    
 decide> The unconnected minima in the chain and their distances are:
     2        1.28     3     4        4.98     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0324 Dev= 0.11% S= 1.29 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.77

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     918 steps. Energy=    -392.6563397       time=       2.63
 Minus side of path:                     939 steps. Energy=    -392.5861740       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.6563397 0.90812E-01     -392.5655276 0.20646E-01     -392.5861740   1.298   1.282   3.666  39.550
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0529 Dev= 0.01% S= 4.99 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   5.12
 isnewts> transition state is the same as number        1 energy=     -392.1894695726
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1488 steps. Energy=    -395.7764936       time=       7.14
 Minus side of path:                     941 steps. Energy=    -392.3677491       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.7764936  3.5870         -392.1894696 0.17828         -392.3677491  21.200  19.477   1.830  79.254
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     246.58    
 decide> The unconnected minima in the chain and their distances are:
     4        4.98     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 4_F using 11 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0124 Dev= 2.26% S= 5.63 time= 6.00
 Following    2 images are candidates for TS:    1    3  
 Converged to TS (number of iterations):         15
 Converged to TS (number of iterations):         31
 DNEB run yielded 2 true transition state(s) time=   6.92
 isnewts> transition state is the same as number        1 energy=     -392.1894695726
 tryconnect> Will not repeat search for TS      2 same as TS      1

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     834 steps. Energy=    -392.1126712       time=       1.88
 Minus side of path:                    1556 steps. Energy=    -395.8412271       time=       6.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.1126712 0.48645E-03     -392.1121847  3.7290         -395.8412271  18.732  18.351   1.755  82.635
        Known (#1)                                              *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      3 steps with      1 missing connections, weight=     369.87    
 decide> The unconnected minima in the chain and their distances are:
     4        4.98     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 4_F using 21 images  (DNEB attempt #3)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 735 RMS= 0.0037 Dev= 4.22% S= 6.08 time= 21.78
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.69
 isnewts> transition state is the same as number        1 energy=     -392.1894695726
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     389.05    
 decide> The unconnected minima in the chain and their distances are:
     5        7.30     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.9819 Dev= 0.04% S= 7.33 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.57

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     827 steps. Energy=    -395.8412271       time=       1.92
 Minus side of path:                     805 steps. Energy=    -395.7764936       time=       1.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.8412271 0.79895E-01     -395.7613320 0.15162E-01     -395.7764936   7.338   7.300   8.941  16.217
        Known (#6)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -392.1126712 0.48645E-03    -392.1121847  3.7290        -395.8412271  18.732  18.351   1.755  82.635
   5     -395.8412271 0.79895E-01    -395.7613320 0.15162E-01    -395.7764936   7.338   7.300   8.941  16.217
   3     -395.7764936  3.5870        -392.1894696 0.17828        -392.3677491  21.200  19.477   1.830  79.254
   1     -392.3677491 0.17828        -392.1894696 0.39670        -392.5861740  10.056   9.154   3.990  36.344
   2     -392.5861740 0.20646E-01    -392.5655276 0.90812E-01    -392.6563397   1.298   1.282   3.666  39.550

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

 Elapsed time=                                90.03
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             37281 time=          51.58 %= 57.3
 OPTIM> # of energy+gradient+Hessian calls=       175 time=           0.85 %=  0.9
