
 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)@comp33.ch.
                 Created on  5/28/12 at 12:50:26 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=    -392.5035088     RMS force=    0.9942306500E-06
 OPTIM> Final energy  =    -392.6505935     RMS force=    0.9678734263E-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=     241.64    
 decide> The unconnected minima in the chain and their distances are:
     2        6.23     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4909 Dev= 0.85% S= 6.76 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        217
 DNEB run yielded 1 true transition state(s) time=  18.00

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     838 steps. Energy=    -391.8054261       time=       2.11
 Minus side of path:                     955 steps. Energy=    -392.6505935       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.8054261 0.74600E-01     -391.7308266 0.91977         -392.6505935  14.110  13.910   3.216  45.081
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     483.27    
 decide> The unconnected minima in the chain and their distances are:
     2        6.23     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 490 RMS= 0.0892 Dev= 5.62% S= 11.48 time= 10.18
 Following    2 images are candidates for TS:    3   12  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=   7.99

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     878 steps. Energy=    -393.8711961       time=       2.15
 Minus side of path:                     872 steps. Energy=    -392.5035088       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.8711961  2.2010         -391.6702079 0.83330         -392.5035088   7.504   6.026   4.679  30.992
        *NEW* (Placed in 4)                                     Known (#1)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     909 steps. Energy=    -392.3317319       time=       2.71
 Minus side of path:                     888 steps. Energy=    -392.6505935       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.3317319  2.7431         -389.5885995  3.0620         -392.6505935   5.976   5.570   4.068  35.643
        *NEW* (Placed in 5)                                     Known (#2)
 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      2 steps with      1 missing connections, weight=     81.081    
 decide> The unconnected minima in the chain and their distances are:
     2        4.33     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 3.9041 Dev= 2.78% S= 4.93 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   5.43

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     852 steps. Energy=    -392.2999114       time=       2.01
 Minus side of path:                     889 steps. Energy=    -392.6505935       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.2999114 0.12810         -392.1718115 0.47878         -392.6505935   6.919   6.566   2.927  49.541
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     162.16    
 decide> The unconnected minima in the chain and their distances are:
     2        4.33     4 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 4_S using 9 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 315 RMS= 0.1984 Dev= 6.13% S= 5.94 time= 4.13
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.43
 isnewts> transition state is the same as number        3 energy=     -389.5885995299
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     895 steps. Energy=    -392.3317319       time=       2.21
 Minus side of path:                     893 steps. Energy=    -392.6505935       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.3317319  2.7431         -389.5885995  3.0620         -392.6505935   5.976   5.570   4.073  35.602
        Known (#5)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     243.24    
 decide> The unconnected minima in the chain and their distances are:
     2        4.33     4 
 

 tryconnect> 630-iteration DNEB run for minima 2_F and 4_S using 18 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 630 RMS= 0.0482 Dev= 4.02% S= 7.29 time= 16.59
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.04
 isnewts> transition state is the same as number        3 energy=     -389.5885995301
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     309.16    
 decide> The unconnected minima in the chain and their distances are:
     6        6.76     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4126 Dev= 0.50% S= 7.14 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.94
 isnewts> transition state is the same as number        4 energy=     -392.1718114895
 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:                     882 steps. Energy=    -392.2999114       time=       2.10
 Minus side of path:                     944 steps. Energy=    -392.6505935       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.2999114 0.12810         -392.1718115 0.47878         -392.6505935   6.920   6.567   2.924  49.593
        Known (#6)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     333.24    
 decide> The unconnected minima in the chain and their distances are:
     5        6.93     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1531 Dev= 0.14% S= 6.97 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.86

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     910 steps. Energy=    -393.8711961       time=       3.05
 Minus side of path:                     910 steps. Energy=    -392.3317319       time=       2.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.8711961  1.9839         -391.8873449 0.44439         -392.3317319   7.124   6.933   2.731  53.100
        Known (#4)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -392.5035088 0.83330        -391.6702079  2.2010        -393.8711961   7.504   6.026   4.679  30.992
   7     -393.8711961  1.9839        -391.8873449 0.44439        -392.3317319   7.124   6.933   2.731  53.100
   3     -392.3317319  2.7431        -389.5885995  3.0620        -392.6505935   5.976   5.570   4.068  35.643

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

 Elapsed time=                               110.88
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             42125 time=          59.48 %= 53.6
 OPTIM> # of energy+gradient+Hessian calls=       371 time=           2.00 %=  1.8
