
 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)@comp29.ch.
                 Created on  5/28/12 at 13: 5:54 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=    -388.5383176     RMS force=    0.8478880402E-06
 OPTIM> Final energy  =    -380.6498804     RMS force=    0.8665655580E-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=     28025.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.37     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 315 RMS= 0.2967 Dev= 1.09% S= 33.28 time= 3.96
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.90

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     943 steps. Energy=    -380.6498804       time=       3.45
 Minus side of path:                     984 steps. Energy=    -382.8934888       time=       3.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.6498804 0.35326E-01     -380.6145542  2.2789         -382.8934888   6.207   5.858   6.054  23.949
        Known (#2)                                              *NEW* (Placed in 3)
 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      2 steps with      1 missing connections, weight=     21049.    
 decide> The unconnected minima in the chain and their distances are:
     3       27.61     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 280 RMS= 0.5536 Dev= 1.37% S= 29.50 time= 3.21
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=   9.58

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     931 steps. Energy=    -389.2003902       time=       3.00
 Minus side of path:                     926 steps. Energy=    -389.2323719       time=       2.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2003902 0.20417E-01     -389.1799733 0.52399E-01     -389.2323719   2.208   2.199   2.965  48.897
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     15222.    
 decide> The unconnected minima in the chain and their distances are:
     3       23.92     5     4       11.53     1 
 

 tryconnect> 245-iteration DNEB run for minima 3_F and 5_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 245 RMS= 2.2591 Dev= 7.53% S= 25.28 time= 2.50
 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=  18.63

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      22.92018318    
 Double-ended search iterations= 105 RMS= 0.6595 Dev= 1.42% S= 11.67 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   5.87

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1030 steps. Energy=    -389.2323719       time=       3.09
 Minus side of path:                     943 steps. Energy=    -388.5383176       time=       3.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2323719  1.9657         -387.2666845  1.2716         -388.5383176  14.538  11.573   2.808  51.640
        Known (#5)                                              Known (#1)
 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=     14967.    
 decide> The unconnected minima in the chain and their distances are:
     3       24.64     4 
 

 tryconnect> 245-iteration DNEB run for minima 3_F and 4_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 245 RMS= 2.3445 Dev= 9.32% S= 26.01 time= 2.50
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   8.90

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     956 steps. Energy=    -389.5605297       time=       3.51
 Minus side of path:                     968 steps. Energy=    -389.2323719       time=       4.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.5605297  1.1050         -388.4555120 0.77686         -389.2323719   5.602   5.479  21.966   6.601
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     14645.    
 decide> The unconnected minima in the chain and their distances are:
     3       24.47     6 
 

 tryconnect> 245-iteration DNEB run for minima 3_F and 6_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      67.04751154    
 Double-ended search iterations= 245 RMS= 1.1562 Dev= 4.13% S= 25.98 time= 2.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   8.90
 isnewts> transition state is the same as number        4 energy=     -388.4555120052
 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:                     975 steps. Energy=    -389.5605297       time=       3.86
 Minus side of path:                     986 steps. Energy=    -389.2323719       time=       3.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.5605297  1.1050         -388.4555120 0.77686         -389.2323719   5.602   5.479  21.944   6.608
        Known (#6)                                              Known (#5)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     18666.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.53     5 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 5_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 272 RMS= 3.5058 Dev= 16.37% S= 27.66 time= 2.68
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        104
 DNEB run yielded 1 true transition state(s) time=   8.82
 isnewts> transition state is the same as number        4 energy=     -388.4555120055
 tryconnect> Will not repeat search for TS      1 same as TS      4
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     19418.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.88     6 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 6_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      70.39988712    
 Double-ended search iterations= 280 RMS= 0.7510 Dev= 1.41% S= 28.60 time= 3.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=   8.30

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1015 steps. Energy=    -383.9401414       time=       2.83
 Minus side of path:                     901 steps. Energy=    -382.8934888       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.9401414  1.2176         -382.7225877 0.17090         -382.8934888  17.572  16.614   5.102  28.420
        *NEW* (Placed in 7)                                     Known (#3)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     17382.    
 decide> The unconnected minima in the chain and their distances are:
     7       25.90     5 
 

 tryconnect> 245-iteration DNEB run for minima 5_S and 7_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 245 RMS= 0.1808 Dev= 0.44% S= 26.94 time= 2.44
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   5.31

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1089 steps. Energy=    -389.2323719       time=       2.85
 Minus side of path:                     949 steps. Energy=    -383.9401414       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2323719  5.6363         -383.5960513 0.34409         -383.9401414  26.661  25.913   3.857  37.597
        Known (#5)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -388.5383176  1.2716        -387.2666845  1.9657        -389.2323719  14.538  11.573   2.808  51.640
   7     -389.2323719  5.6363        -383.5960513 0.34409        -383.9401414  26.661  25.913   3.857  37.597
   6     -383.9401414  1.2176        -382.7225877 0.17090        -382.8934888  17.572  16.614   5.102  28.420
   1     -382.8934888  2.2789        -380.6145542 0.35326E-01    -380.6498804   6.207   5.858   6.054  23.949

 Number of TS in the path       =      4
 Number of cycles               =      8

 Elapsed time=                               148.78
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             40279 time=          55.13 %= 37.1
 OPTIM> # of energy+gradient+Hessian calls=       832 time=           4.20 %=  2.8
