
 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)@comp28.ch.
                 Created on  5/28/12 at 12:47:21 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -383.9108846     RMS force=    0.9184736574E-06
 OPTIM> Final energy  =    -388.6148381     RMS force=    0.9673031405E-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=     29549.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.92     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      41.16135595    
 Double-ended search iterations= 315 RMS= 2.6615 Dev= 1.85% S= 31.36 time= 4.02
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   8.32

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     900 steps. Energy=    -388.4709944       time=       2.06
 Minus side of path:                     916 steps. Energy=    -388.5644990       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4709944 0.17456E-01     -388.4535381 0.11096         -388.5644990   1.047   1.044  40.204   3.607
        *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=     26193.    
 decide> The unconnected minima in the chain and their distances are:
     2        2.24     4     3       29.69     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0131 Dev= 0.22% S= 2.24 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     937 steps. Energy=    -388.6148381       time=       3.00
 Minus side of path:                     911 steps. Energy=    -388.5644990       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6148381 0.57389E-01     -388.5574487 0.70503E-02     -388.5644990   2.242   2.239   3.162  45.853
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      63.85477290    
 Double-ended search iterations= 280 RMS= 0.4101 Dev= 0.78% S= 29.98 time= 3.24
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        154
 DNEB run yielded 1 true transition state(s) time=  10.31

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1054 steps. Energy=    -388.1426005       time=       3.21
 Minus side of path:                    1456 steps. Energy=    -388.5644990       time=       6.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1426005  4.5386         -383.6039685  4.9605         -388.5644990  51.006  44.254   2.937  49.376
        *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=     11027.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.26     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 210 RMS= 0.1576 Dev= 0.88% S= 22.60 time= 1.83
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   7.68
 isnewts> transition state is the same as number        3 energy=     -383.6039684950
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1066 steps. Energy=    -388.1426005       time=       2.84
 Minus side of path:                    1443 steps. Energy=    -388.5644990       time=       5.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1426005  4.5386         -383.6039685  4.9605         -388.5644990  51.010  44.245   2.949  49.177
        Known (#5)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     22054.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.26     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 805 RMS= 0.0405 Dev= 7.87% S= 31.06 time= 26.21
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   4.87
 isnewts> transition state is the same as number        3 energy=     -383.6039684949
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     27405.    
 decide> The unconnected minima in the chain and their distances are:
     4       30.15     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 4_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      67.04751154    
 Double-ended search iterations= 315 RMS= 0.8216 Dev= 1.34% S= 30.46 time= 4.00
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   8.19
 isnewts> transition state is the same as number        1 energy=     -388.4535381477
 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:                     931 steps. Energy=    -388.4709944       time=       2.51
 Minus side of path:                     937 steps. Energy=    -388.5644990       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4709944 0.17456E-01     -388.4535381 0.11096         -388.5644990   1.047   1.044  40.204   3.607
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     52363.    
 decide> The unconnected minima in the chain and their distances are:
     3       29.69     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 805 RMS= 0.0275 Dev= 1.52% S= 32.08 time= 26.38
 Following    2 images are candidates for TS:    1    5  
 Converged to TS (number of iterations):         18
 Converged to TS (number of iterations):         80
 DNEB run yielded 2 true transition state(s) time=  11.40

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     945 steps. Energy=    -383.9108846       time=       3.74
 Minus side of path:                    1480 steps. Energy=    -388.5644990       time=       7.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.9108846 0.40080E-01     -383.8708044  4.6937         -388.5644990  31.618  30.185   2.879  50.363
        Known (#1)                                              Known (#4)

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1615 steps. Energy=    -388.5644990       time=       8.62
 Minus side of path:                     966 steps. Energy=    -384.8741448       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5644990  4.0376         -384.5269072 0.34724         -384.8741448  42.426  36.013   2.712  53.457
        Known (#4)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -383.9108846 0.40080E-01    -383.8708044  4.6937        -388.5644990  31.618  30.185   2.879  50.363
   2     -388.5644990 0.70503E-02    -388.5574487 0.57389E-01    -388.6148381   2.242   2.239   3.162  45.853

 Number of TS in the path       =      2
 Number of cycles               =      6

 Elapsed time=                               176.88
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             70072 time=          95.66 %= 54.1
 OPTIM> # of energy+gradient+Hessian calls=       555 time=           2.56 %=  1.4
