
 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)@comp23.ch.
                 Created on  5/28/12 at 12:49:35 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -386.9950363     RMS force=    0.9442932671E-06
 OPTIM> Final energy  =    -394.0946509     RMS force=    0.8441807438E-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=     77222.    
 decide> The unconnected minima in the chain and their distances are:
     2       42.58     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2981058282    
 Double-ended search iterations= 420 RMS= 0.0960 Dev= 4.20% S= 49.48 time= 7.03
 Following    1 images are candidates for TS:    7  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  40.57
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.15444E+06
 decide> The unconnected minima in the chain and their distances are:
     2       42.58     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 805 RMS= 0.0520 Dev= 5.40% S= 53.17 time= 26.03
 Following    3 images are candidates for TS:    1   10   13  
 Converged to TS (number of iterations):         24
 Converged to TS (number of iterations):         75
 Converged to TS (number of iterations):        242
 DNEB run yielded 3 true transition state(s) time=  30.02

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     957 steps. Energy=    -386.9950363       time=       2.67
 Minus side of path:                     931 steps. Energy=    -391.9281723       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9950363  1.0861         -385.9089241  6.0192         -391.9281723   6.996   5.596  13.811  10.499
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1043 steps. Energy=    -391.9279111       time=       2.76
 Minus side of path:                    1026 steps. Energy=    -390.8573318       time=       2.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9279111  2.8950         -389.0329029  1.8244         -390.8573318  36.401  32.093   3.744  38.730
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1320 steps. Energy=    -397.5605733       time=       4.77
 Minus side of path:                     901 steps. Energy=    -388.6881227       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5605733  8.9174         -388.6431809 0.44942E-01     -388.6881227  30.935  30.300   1.876  77.273
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     4082.0    
 decide> The unconnected minima in the chain and their distances are:
     2       15.86     5     4        4.55     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 5_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 140 RMS= 0.2196 Dev= 0.67% S= 16.94 time= 0.75
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   4.55

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     977 steps. Energy=    -390.7971746       time=       2.28
 Minus side of path:                     923 steps. Energy=    -390.8573318       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7971746 0.18429         -390.6128853 0.24445         -390.8573318   7.734   7.134   2.456  59.045
        *NEW* (Placed in 8)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0458 Dev= 0.07% S= 4.58 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.84

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     919 steps. Energy=    -391.9281723       time=       2.19
 Minus side of path:                     882 steps. Energy=    -391.9279111       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9281723 0.42375E-01     -391.8857972 0.42114E-01     -391.9279111   4.652   4.552  11.857  12.229
        Known (#3)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1415.3    
 decide> The unconnected minima in the chain and their distances are:
     2       11.23     8 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 105 RMS= 0.8008 Dev= 0.37% S= 12.13 time= 0.42
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        188
 DNEB run yielded 1 true transition state(s) time=  13.69

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     946 steps. Energy=    -387.1482417       time=       2.14
 Minus side of path:                    1140 steps. Energy=    -390.7971746       time=       2.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1482417  1.0113         -386.1369747  4.6602         -390.7971746  39.616  36.846   3.210  45.171
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2830.6    
 decide> The unconnected minima in the chain and their distances are:
     2       11.23     8 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 8_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 805 RMS= 0.0333 Dev= 4.47% S= 17.40 time= 24.39
 Following    2 images are candidates for TS:   12   19  
 Converged to TS (number of iterations):        171
 Converged to TS (number of iterations):         13
 DNEB run yielded 2 true transition state(s) time=  15.40

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     927 steps. Energy=    -396.2474142       time=       2.13
 Minus side of path:                     926 steps. Energy=    -394.0946509       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.2474142  2.2343         -394.0131071 0.81544E-01     -394.0946509  12.571  12.351   3.175  45.664
        *NEW* (Placed in 10)                                    Known (#2)
 Unconnected minimum 10 found its way to F set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     965 steps. Energy=    -390.7971746       time=       2.24
 Minus side of path:                     922 steps. Energy=    -391.4223786       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7971746  2.8457         -387.9514497  3.4709         -391.4223786   7.521   5.649   5.334  27.185
        Known (#8)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     307.52    
 decide> The unconnected minima in the chain and their distances are:
     2        6.75    11 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.7043 Dev= 2.14% S= 7.11 time= 0.19
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  36.34
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     615.03    
 decide> The unconnected minima in the chain and their distances are:
     2        6.75    11 
 

 tryconnect> 525-iteration DNEB run for minima 2_F and 11_S using 15 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 525 RMS= 0.0276 Dev= 5.49% S= 9.05 time= 10.46
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.81

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     944 steps. Energy=    -391.4223786       time=       2.83
 Minus side of path:                     929 steps. Energy=    -394.0946509       time=       2.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4223786  5.3114         -386.1109490  7.9837         -394.0946509  15.588   6.751   6.824  21.250
        Known (#11)                                             Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -386.9950363  1.0861        -385.9089241  6.0192        -391.9281723   6.996   5.596  13.811  10.499
   5     -391.9281723 0.42375E-01    -391.8857972 0.42114E-01    -391.9279111   4.652   4.552  11.857  12.229
   2     -391.9279111  2.8950        -389.0329029  1.8244        -390.8573318  36.401  32.093   3.744  38.730
   4     -390.8573318 0.24445        -390.6128853 0.18429        -390.7971746   7.734   7.134   2.456  59.045
   8     -390.7971746  2.8457        -387.9514497  3.4709        -391.4223786   7.521   5.649   5.334  27.185
   9     -391.4223786  5.3114        -386.1109490  7.9837        -394.0946509  15.588   6.751   6.824  21.250

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               263.29
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             85418 time=         113.60 %= 43.1
 OPTIM> # of energy+gradient+Hessian calls=      1311 time=           6.00 %=  2.3
