
 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)@comp35.ch.
                 Created on  5/28/12 at 12:46:53 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=    -386.5131680     RMS force=    0.9503510252E-06
 OPTIM> Final energy  =    -387.4391512     RMS force=    0.8762285236E-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=     116.63    
 decide> The unconnected minima in the chain and their distances are:
     2        4.89     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.6217 Dev= 1.78% S= 5.45 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   6.71

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1650 steps. Energy=    -398.0288945       time=       8.85
 Minus side of path:                     952 steps. Energy=    -386.5131680       time=       3.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.0288945  12.505         -385.5235323 0.98964         -386.5131680  52.976  43.811   2.399  60.445
        *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      1 steps with      1 missing connections, weight=     233.27    
 decide> The unconnected minima in the chain and their distances are:
     2        4.89     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 385 RMS= 0.6687 Dev= 4.45% S= 7.83 time= 5.79
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.60

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     947 steps. Energy=    -387.4391512       time=       3.22
 Minus side of path:                     928 steps. Energy=    -387.4391512       time=       2.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4391512  6.3881         -381.0510152  6.3881         -387.4391512   8.419   2.939  47.408   3.059
        Known (#2)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     349.90    
 decide> The unconnected minima in the chain and their distances are:
     2        4.89     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 2_F using 21 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 735 RMS= 0.1573 Dev= 4.71% S= 7.40 time= 20.69
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.16
 isnewts> transition state is the same as number        2 energy=     -381.0510151833
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     954 steps. Energy=    -387.4391512       time=       2.84
 Minus side of path:                     957 steps. Energy=    -387.4391512       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4391512  6.3881         -381.0510152  6.3881         -387.4391512   8.415   2.930  48.086   3.015
        Known (#2)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 3 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     76954.    
 decide> The unconnected minima in the chain and their distances are:
     2       42.53     3 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 3_S using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      77.61587555    
 Double-ended search iterations= 420 RMS= 1.1300 Dev= 0.97% S= 44.73 time= 7.30
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        134
 DNEB run yielded 1 true transition state(s) time=  12.27

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     942 steps. Energy=    -387.3425696       time=       3.12
 Minus side of path:                    1234 steps. Energy=    -390.5776719       time=       4.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3425696 0.69177         -386.6507973  3.9269         -390.5776719  31.270  27.973   2.475  58.590
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     669.73    
 decide> The unconnected minima in the chain and their distances are:
     2        4.49     4     4        8.33     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= 0.0286 Dev= 0.07% S= 4.50 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=   3.56

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     897 steps. Energy=    -387.4391512       time=       2.55
 Minus side of path:                     881 steps. Energy=    -387.3980381       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4391512 0.70066E-01     -387.3690848 0.28953E-01     -387.3980381   0.735   0.729  23.317   6.219
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.5432 Dev= 0.96% S= 8.80 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.44

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     822 steps. Energy=    -386.4599995       time=       2.27
 Minus side of path:                     907 steps. Energy=    -386.5131680       time=       2.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.4599995 0.22519E-01     -386.4374805 0.75687E-01     -386.5131680   0.717   0.710  22.910   6.329
        *NEW* (Placed in 7)                                     Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     115.58    
 decide> The unconnected minima in the chain and their distances are:
     6        4.87     7 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.6995 Dev= 1.18% S= 5.48 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   6.62

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1602 steps. Energy=    -398.0480113       time=       9.04
 Minus side of path:                     930 steps. Energy=    -386.4599995       time=       3.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.0480113  12.546         -385.5017785 0.95822         -386.4599995  52.634  43.650   2.400  60.423
        *NEW* (Placed in 8)                                     Known (#7)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     118.27    
 decide> The unconnected minima in the chain and their distances are:
     6        4.91     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.6002 Dev= 1.30% S= 5.53 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   5.38
 isnewts> transition state is the same as number        6 energy=     -386.4374805000
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     909 steps. Energy=    -386.5131680       time=       3.60
 Minus side of path:                     862 steps. Energy=    -386.4599995       time=       2.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.5131680 0.75687E-01     -386.4374805 0.22519E-01     -386.4599995   0.717   0.710  22.908   6.330
        Known (#1)                                              Known (#7)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     121.54    
 decide> The unconnected minima in the chain and their distances are:
     2        4.95     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.7506 Dev= 2.23% S= 5.53 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.62
 isnewts> transition state is the same as number        6 energy=     -386.4374805000
 tryconnect> Will not repeat search for TS      1 same as TS      6
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     231.15    
 decide> The unconnected minima in the chain and their distances are:
     6        4.87     7 
 

 tryconnect> 385-iteration DNEB run for minima 6_F and 7_S using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 385 RMS= 0.0768 Dev= 4.95% S= 7.57 time= 5.78
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     939 steps. Energy=    -387.3980381       time=       2.88
 Minus side of path:                     939 steps. Energy=    -387.3980381       time=       3.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3980381  6.3814         -381.0166229  6.3814         -387.3980381   8.414   2.928  48.221   3.007
        Known (#6)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 8 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     236.54    
 decide> The unconnected minima in the chain and their distances are:
     6        4.91     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 6_F using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 385 RMS= 0.1115 Dev= 4.74% S= 7.50 time= 5.75
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.96
 isnewts> transition state is the same as number        2 energy=     -381.0510151830
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 8 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     243.07    
 decide> The unconnected minima in the chain and their distances are:
     2        4.95     7 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 7_S using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 385 RMS= 0.1457 Dev= 4.24% S= 7.40 time= 5.67
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.00
 isnewts> transition state is the same as number        2 energy=     -381.0510151832
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 8 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     346.73    
 decide> The unconnected minima in the chain and their distances are:
     6        4.87     7 
 

 tryconnect> 700-iteration DNEB run for minima 6_F and 7_S using 20 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      24.06619234    
 Double-ended search iterations= 700 RMS= 0.1993 Dev= 4.92% S= 7.75 time= 18.62
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.14
 isnewts> transition state is the same as number        9 energy=     -381.0166228902
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     942 steps. Energy=    -387.3980381       time=       2.90
 Minus side of path:                     963 steps. Energy=    -387.3980381       time=       3.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3980381  6.3814         -381.0166229  6.3814         -387.3980381   8.414   2.929  48.094   3.015
        Known (#6)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 13 >>>>>>>>>>>>>>>>>>>>> 8 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     354.82    
 decide> The unconnected minima in the chain and their distances are:
     6        4.91     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 6_F using 21 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      37.33456322    
 Double-ended search iterations= 735 RMS= 0.2366 Dev= 5.05% S= 8.08 time= 20.93
 Following    2 images are candidates for TS:    7   12  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         26
 DNEB run yielded 2 true transition state(s) time=   9.20
 isnewts> transition state is the same as number        2 energy=     -381.0510151833
 tryconnect> Will not repeat search for TS      2 same as TS      2

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     932 steps. Energy=    -387.4391512       time=       2.32
 Minus side of path:                     897 steps. Energy=    -386.5131680       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4391512  3.5973         -383.8418460  2.6713         -386.5131680   7.262   5.087  12.597  11.511
        Known (#2)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  11     -386.5131680  2.6713        -383.8418460  3.5973        -387.4391512   7.262   5.087  12.597  11.511

 Number of TS in the path       =      1
 Number of cycles               =     13

 Elapsed time=                               245.61
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            104192 time=         137.41 %= 55.9
 OPTIM> # of energy+gradient+Hessian calls=       507 time=           2.73 %=  1.1
