
 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)@comp24.ch.
                 Created on  5/28/12 at 13:10:35 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -394.5890829     RMS force=    0.8668942108E-06
 OPTIM> Final energy  =    -401.3454376     RMS force=    0.9309026839E-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=     15554.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.96     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.8734 Dev= 2.14% S= 27.77 time= 2.80
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.95

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     961 steps. Energy=    -396.9896486       time=       3.48
 Minus side of path:                     977 steps. Energy=    -394.5890829       time=       3.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.9896486  5.8055         -391.1841375  3.4049         -394.5890829  12.172  11.488  22.297   6.503
        *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=     6559.4    
 decide> The unconnected minima in the chain and their distances are:
     2       18.72     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1846 Dev= 0.28% S= 19.62 time= 1.45
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  26.46
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     13119.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.72     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.5098621309    
 Double-ended search iterations= 805 RMS= 0.1846 Dev= 39.64% S= 30.97 time= 28.11
 Following    3 images are candidates for TS:    8   12   23  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         20
 DNEB run yielded 2 true transition state(s) time=  31.94

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     809 steps. Energy=    -401.3454376       time=       1.98
 Minus side of path:                     789 steps. Energy=    -400.7373619       time=       1.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.3454376  2.9319         -398.4135587  2.3238         -400.7373619   9.312   8.275  27.250   5.321
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1004 steps. Energy=    -401.6605666       time=       3.07
 Minus side of path:                     873 steps. Energy=    -396.9896486       time=       2.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.6605666  4.6748         -396.9857707 0.38779E-02     -396.9896486  17.813  17.575   4.499  32.230
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     132.48    
 decide> The unconnected minima in the chain and their distances are:
     4        5.10     5 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.5814 Dev= 1.49% S= 5.66 time= 0.28
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  25.36
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     184.21    
 decide> The unconnected minima in the chain and their distances are:
     2        5.69     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.5640 Dev= 0.25% S= 6.41 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.15

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     766 steps. Energy=    -401.3454376       time=       1.74
 Minus side of path:                     768 steps. Energy=    -401.3715356       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.3454376 0.39786E-01     -401.3056512 0.65884E-01     -401.3715356   0.854   0.851  35.421   4.094
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     190.08    
 decide> The unconnected minima in the chain and their distances are:
     6        5.75     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 1.6783 Dev= 0.96% S= 6.48 time= 0.28
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.18
 isnewts> transition state is the same as number        4 energy=     -401.3056512106
 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:                     760 steps. Energy=    -401.3454376       time=       1.74
 Minus side of path:                     799 steps. Energy=    -401.3715356       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.3454376 0.39786E-01     -401.3056512 0.65884E-01     -401.3715356   0.854   0.851  35.424   4.093
        Known (#2)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     264.97    
 decide> The unconnected minima in the chain and their distances are:
     4        5.10     5 
 

 tryconnect> 385-iteration DNEB run for minima 4_F and 5_S using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 385 RMS= 0.0766 Dev= 8.53% S= 7.14 time= 6.55
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.85

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     801 steps. Energy=    -401.6605666       time=       2.57
 Minus side of path:                     819 steps. Energy=    -401.3454376       time=       2.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.6605666  5.0275         -396.6330266  4.7124         -401.3454376   6.559   5.694  36.981   3.921
        Known (#5)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -394.5890829  3.4049        -391.1841375  5.8055        -396.9896486  12.172  11.488  22.297   6.503
   3     -396.9896486 0.38779E-02    -396.9857707  4.6748        -401.6605666  17.813  17.575   4.499  32.230
   6     -401.6605666  5.0275        -396.6330266  4.7124        -401.3454376   6.559   5.694  36.981   3.921

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

 Elapsed time=                               169.50
 OPTIM> # of energy calls=                        104 time=           0.15 %=  0.1
 OPTIM> # of energy+gradient calls=             46848 time=          69.19 %= 40.8
 OPTIM> # of energy+gradient+Hessian calls=       913 time=           5.27 %=  3.1
