
 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: 3:40 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=    -399.4433289     RMS force=    0.8667251535E-06
 OPTIM> Final energy  =    -388.3743583     RMS force=    0.9589739517E-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=     84690.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.91     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0834 Dev= 4.00% S= 55.81 time= 8.37
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.82

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1196 steps. Energy=    -394.3983805       time=       3.62
 Minus side of path:                     917 steps. Energy=    -388.3743583       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.3983805  6.3778         -388.0205580 0.35380         -388.3743583  29.211  27.403   1.977  73.341
        *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      2 steps with      1 missing connections, weight=     14103.    
 decide> The unconnected minima in the chain and their distances are:
     3       24.16     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.3835 Dev= 0.47% S= 26.03 time= 2.48
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   5.74

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     906 steps. Energy=    -396.6857038       time=       2.60
 Minus side of path:                     911 steps. Energy=    -394.3983805       time=       3.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6857038  3.1084         -393.5772961 0.82108         -394.3983805  14.167  12.922   6.811  21.288
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     9892.3    
 decide> The unconnected minima in the chain and their distances are:
     4       21.47     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2425 Dev= 0.46% S= 23.32 time= 1.88
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   5.52

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1052 steps. Energy=    -396.1464806       time=       3.60
 Minus side of path:                    1040 steps. Energy=    -397.9716366       time=       3.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  1.0069         -395.1395357  2.8321         -397.9716366  23.255   7.484   9.559  15.169
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     9202.1    
 decide> The unconnected minima in the chain and their distances are:
     4       20.95     6     5        2.33     1 
 

 tryconnect> 210-iteration DNEB run for minima 4_F and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1234 Dev= 0.25% S= 22.02 time= 1.86
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   5.47

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     926 steps. Energy=    -397.5139278       time=       3.21
 Minus side of path:                     892 steps. Energy=    -397.5322550       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5139278 0.38865E-01     -397.4750629 0.57192E-01     -397.5322550   1.244   1.242   4.239  34.205
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.2385 Dev= 8.19% S= 2.74 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=   8.23

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     905 steps. Energy=    -396.1464806       time=       2.62
 Minus side of path:                     845 steps. Energy=    -395.5808440       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806 0.62640         -395.5200832 0.60761E-01     -395.5808440  10.397  10.130   5.581  25.983
        Known (#5)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     3982.0    
 decide> The unconnected minima in the chain and their distances are:
     4       12.23     7     7       12.86     9     5        2.33     1 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0691 Dev= 0.06% S= 12.29 time= 0.53
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   5.38

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     836 steps. Energy=    -396.7931836       time=       2.08
 Minus side of path:                     871 steps. Energy=    -397.5322550       time=       2.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.7931836 0.62676         -396.1664218  1.3658         -397.5322550  11.044  10.906   2.724  53.224
        *NEW* (Placed in 10)                                    Known (#8)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 7_U and 9_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1753 Dev= 0.27% S= 13.20 time= 0.50
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.93
 isnewts> transition state is the same as number        3 energy=     -395.1395357468
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1028 steps. Energy=    -396.1464806       time=       3.47
 Minus side of path:                    1045 steps. Energy=    -397.9716366       time=       3.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  1.0069         -395.1395357  2.8321         -397.9716366  23.255   7.484   9.551  15.182
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_U using 5 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 175 RMS= 0.4191 Dev= 4.90% S= 2.86 time= 1.35
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.53

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     870 steps. Energy=    -396.1464806       time=       3.10
 Minus side of path:                     830 steps. Energy=    -399.4433289       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  3.7716         -392.3749287  7.0684         -399.4433289   4.422   2.329  35.210   4.118
        Known (#5)                                              Known (#1)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     2224.3    
 decide> The unconnected minima in the chain and their distances are:
     4        3.91    10     8       12.94     9 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0784 Dev= 0.04% S= 3.92 time= 0.27
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.22

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     881 steps. Energy=    -396.7931836       time=       2.12
 Minus side of path:                     862 steps. Energy=    -396.6702512       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.7931836 0.13711         -396.6560690 0.14182E-01     -396.6702512   2.561   2.556   2.724  53.223
        Known (#10)                                             *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 8_U and 9_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1436 Dev= 0.36% S= 13.28 time= 0.51
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.60
 isnewts> transition state is the same as number        3 energy=     -395.1395357477
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     2688.2    
 decide> The unconnected minima in the chain and their distances are:
     4        1.56    11     8       13.90     6 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0107 Dev= 0.00% S= 1.56 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.01

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     841 steps. Energy=    -396.6857038       time=       2.56
 Minus side of path:                     843 steps. Energy=    -396.6702512       time=       2.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6857038 0.28667E-01     -396.6570369 0.13214E-01     -396.6702512   1.566   1.563   2.266  63.999
        Known (#4)                                              Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 6_S and 8_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1060 Dev= 0.05% S= 14.08 time= 0.88
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.22

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     908 steps. Energy=    -397.5322550       time=       2.64
 Minus side of path:                    1031 steps. Energy=    -397.9716366       time=       2.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5322550 0.59115         -396.9411086  1.0305         -397.9716366  15.018  13.898   2.548  56.908
        Known (#8)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -399.4433289  7.0684        -392.3749287  3.7716        -396.1464806   4.422   2.329  35.210   4.118
   3     -396.1464806  1.0069        -395.1395357  2.8321        -397.9716366  23.255   7.484   9.559  15.169
  11     -397.9716366  1.0305        -396.9411086 0.59115        -397.5322550  15.018  13.898   2.548  56.908
   6     -397.5322550  1.3658        -396.1664218 0.62676        -396.7931836  11.044  10.906   2.724  53.224
   9     -396.7931836 0.13711        -396.6560690 0.14182E-01    -396.6702512   2.561   2.556   2.724  53.223
  10     -396.6702512 0.13214E-01    -396.6570369 0.28667E-01    -396.6857038   1.566   1.563   2.266  63.999
   2     -396.6857038  3.1084        -393.5772961 0.82108        -394.3983805  14.167  12.922   6.811  21.288
   1     -394.3983805  6.3778        -388.0205580 0.35380        -388.3743583  29.211  27.403   1.977  73.341

 Number of TS in the path       =      8
 Number of cycles               =      7

 Elapsed time=                               139.53
 OPTIM> # of energy calls=                        112 time=           0.15 %=  0.1
 OPTIM> # of energy+gradient calls=             44531 time=          61.20 %= 43.9
 OPTIM> # of energy+gradient+Hessian calls=       423 time=           2.11 %=  1.5
