
 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 13: 7: 0 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -388.8174209     RMS force=    0.9142892131E-06
 OPTIM> Final energy  =    -385.4791588     RMS force=    0.9033076212E-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=     11171.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.35     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0619 Dev= 0.09% S= 23.11 time= 1.70
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        138
 DNEB run yielded 1 true transition state(s) time=  12.51

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1161 steps. Energy=    -394.6417674       time=       4.67
 Minus side of path:                     955 steps. Energy=    -386.9948355       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6417674  7.7881         -386.8536333 0.14120         -386.9948355  23.016  21.845   2.386  60.765
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     22341.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.35     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3804669723    
 Double-ended search iterations= 805 RMS= 0.0807 Dev= 4.80% S= 29.01 time= 24.27
 Following    2 images are candidates for TS:   13   17  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):        116
 DNEB run yielded 1 true transition state(s) time=  29.26
 isnewts> transition state is the same as number        1 energy=     -386.8536333441
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     953 steps. Energy=    -386.9948355       time=       2.51
 Minus side of path:                    1150 steps. Energy=    -394.6417674       time=       4.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9948355 0.14120         -386.8536333  7.7881         -394.6417674  23.013  21.841   2.388  60.720
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     23588.    
 decide> The unconnected minima in the chain and their distances are:
     2       15.99     4     4       26.92     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.0646 Dev= 0.29% S= 16.08 time= 0.77
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   6.87

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     947 steps. Energy=    -386.9948355       time=       2.55
 Minus side of path:                     903 steps. Energy=    -385.8162135       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9948355  1.1844         -385.8103897 0.58238E-02     -385.8162135  12.616  12.562   5.646  25.682
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 4_U using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.168613344    
 Double-ended search iterations= 280 RMS= 0.0878 Dev= 0.10% S= 28.29 time= 3.00
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=   8.30
 isnewts> transition state is the same as number        1 energy=     -386.8536333442
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     21159.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.19     5     5       27.32     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1257 Dev= 0.01% S= 9.21 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.05

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     921 steps. Energy=    -385.4791588       time=       2.44
 Minus side of path:                     922 steps. Energy=    -385.8162135       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4791588 0.22210E-01     -385.4569492 0.35926         -385.8162135   9.369   9.188   6.202  23.381
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 5_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.059966752    
 Double-ended search iterations= 280 RMS= 0.0500 Dev= 0.27% S= 28.55 time= 2.98
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=   8.98
 isnewts> transition state is the same as number        1 energy=     -386.8536333443
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     39002.    
 decide> The unconnected minima in the chain and their distances are:
     4       26.92     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 805 RMS= 0.0220 Dev= 4.06% S= 34.43 time= 25.15
 Following    1 images are candidates for TS:   19  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.82
 isnewts> transition state is the same as number        1 energy=     -386.8536333439
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     40766.    
 decide> The unconnected minima in the chain and their distances are:
     5       27.32     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 805 RMS= 0.0213 Dev= 4.38% S= 35.85 time= 24.24
 Following    3 images are candidates for TS:   15   19   23  
 Converged to TS (number of iterations):        128
 Converged to TS (number of iterations):         68
 Converged to TS (number of iterations):         21
 DNEB run yielded 3 true transition state(s) time=  23.70
 isnewts> transition state is the same as number        1 energy=     -386.8536333442
 tryconnect> Will not repeat search for TS      2 same as TS      1
 isnewts> transition state is the same as number        3 energy=     -385.8103897449
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1022 steps. Energy=    -391.6351044       time=       2.67
 Minus side of path:                     870 steps. Energy=    -387.9455983       time=       1.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.6351044  3.6903         -387.9447740 0.82426E-03     -387.9455983  15.479  15.406   2.438  59.483
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     976 steps. Energy=    -386.9948355       time=       2.90
 Minus side of path:                     917 steps. Energy=    -385.8162135       time=       3.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9948355  1.1844         -385.8103897 0.58238E-02     -385.8162135  12.616  12.562   5.643  25.696
        Known (#4)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     20640.    
 decide> The unconnected minima in the chain and their distances are:
     3        6.20     6     7       27.32     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2332 Dev= 0.41% S= 6.35 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   5.20

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     926 steps. Energy=    -394.6417674       time=       3.70
 Minus side of path:                     955 steps. Energy=    -391.6351044       time=       2.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6417674  4.1434         -390.4984037  1.1367         -391.6351044   7.037   6.200  14.243  10.180
        Known (#3)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 7_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1057 Dev= 0.25% S= 28.53 time= 3.05
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.54

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     975 steps. Energy=    -388.6935909       time=       2.58
 Minus side of path:                     936 steps. Energy=    -387.9455983       time=       3.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6935909  1.0893         -387.6042476 0.34135         -387.9455983  22.957  21.851   3.072  47.208
        *NEW* (Placed in 8)                                     Known (#7)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1500.2    
 decide> The unconnected minima in the chain and their distances are:
     8       11.45     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 8_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0816 Dev= 0.06% S= 11.50 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.75

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     919 steps. Energy=    -388.8174209       time=       2.78
 Minus side of path:                     961 steps. Energy=    -388.6078406       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.8174209 0.24241         -388.5750149 0.32826E-01     -388.6078406   5.971   5.803   3.544  40.912
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 9 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     269.37    
 decide> The unconnected minima in the chain and their distances are:
     8        6.46     9 
 

 tryconnect> 70-iteration DNEB run for minima 8_F and 9_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0628 Dev= 0.01% S= 6.47 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.94

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     881 steps. Energy=    -388.6078406       time=       1.98
 Minus side of path:                     929 steps. Energy=    -388.6935909       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6078406 0.35417E-02     -388.6042989 0.89292E-01     -388.6935909   6.518   6.458   8.916  16.263
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -388.8174209 0.24241        -388.5750149 0.32826E-01    -388.6078406   5.971   5.803   3.544  40.912
  10     -388.6078406 0.35417E-02    -388.6042989 0.89292E-01    -388.6935909   6.518   6.458   8.916  16.263
   8     -388.6935909  1.0893        -387.6042476 0.34135        -387.9455983  22.957  21.851   3.072  47.208
   5     -387.9455983 0.82426E-03    -387.9447740  3.6903        -391.6351044  15.479  15.406   2.438  59.483
   7     -391.6351044  1.1367        -390.4984037  4.1434        -394.6417674   7.037   6.200  14.243  10.180
   1     -394.6417674  7.7881        -386.8536333 0.14120        -386.9948355  23.016  21.845   2.386  60.765
   3     -386.9948355  1.1844        -385.8103897 0.58238E-02    -385.8162135  12.616  12.562   5.646  25.682
   4     -385.8162135 0.35926        -385.4569492 0.22210E-01    -385.4791588   9.369   9.188   6.202  23.381

 Number of TS in the path       =      8
 Number of cycles               =      9

 Elapsed time=                               266.11
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            100086 time=         128.01 %= 48.1
 OPTIM> # of energy+gradient+Hessian calls=      1226 time=           6.19 %=  2.3
