
 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)@comp34.ch.
                 Created on  5/28/12 at 13:13:14 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=    -385.8079668     RMS force=    0.9722541170E-06
 OPTIM> Final energy  =    -385.2626841     RMS force=    0.9578389499E-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=     1067.2    
 decide> The unconnected minima in the chain and their distances are:
     2       10.22     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 105 RMS= 0.5307 Dev= 1.14% S= 14.96 time= 0.38
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.20

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1024 steps. Energy=    -385.2626841       time=       3.44
 Minus side of path:                    1970 steps. Energy=    -383.9142203       time=      14.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2626841  6.8018         -378.4609317  5.4533         -383.9142203  65.817  59.047   1.792  80.901
        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      1 steps with      1 missing connections, weight=     2134.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.22     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      3.589423646    
 Double-ended search iterations= 805 RMS= 0.0703 Dev= 4.73% S= 22.09 time= 20.52
 Following    3 images are candidates for TS:    2   11   17  
 Converged to TS (number of iterations):         15
 Converged to TS (number of iterations):         70
 Converged to TS (number of iterations):         27
 DNEB run yielded 3 true transition state(s) time=  16.99

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     991 steps. Energy=    -385.8079668       time=       3.16
 Minus side of path:                    1003 steps. Energy=    -386.8129981       time=       3.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8079668  2.5002         -383.3077684  3.5052         -386.8129981   5.606   5.414   7.466  19.421
        Known (#1)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1214 steps. Energy=    -381.1556837       time=       3.63
 Minus side of path:                    1121 steps. Energy=    -383.7749650       time=       3.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1556837 0.73968         -380.4160082  3.3590         -383.7749650  37.211  31.955   2.006  72.296
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1017 steps. Energy=    -379.6292852       time=       3.32
 Minus side of path:                    1026 steps. Energy=    -381.5270744       time=       2.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6292852 0.94401         -378.6852711  2.8418         -381.5270744   6.590   6.170  27.822   5.212
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     529.10    
 decide> The unconnected minima in the chain and their distances are:
     2        8.09     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 0.8154 Dev= 1.76% S= 8.67 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   3.69

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1008 steps. Energy=    -387.1186528       time=       2.18
 Minus side of path:                    1005 steps. Energy=    -385.2626841       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1186528  4.8706         -382.2480505  3.0146         -385.2626841  12.088   4.668   3.230  44.895
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1029.5    
 decide> The unconnected minima in the chain and their distances are:
     9       10.10     4 
 

 tryconnect> 105-iteration DNEB run for minima 4_S and 9_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 105 RMS= 0.3867 Dev= 0.89% S= 10.58 time= 0.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   3.95

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     982 steps. Energy=    -386.8129981       time=       2.03
 Minus side of path:                     998 steps. Energy=    -387.8018809       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8129981 0.69984E-01     -386.7430140  1.0589         -387.8018809  10.124   9.541   1.679  86.368
        Known (#4)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     128.13    
 decide> The unconnected minima in the chain and their distances are:
     9        5.04    10 
 

 tryconnect> 70-iteration DNEB run for minima 9_F and 10_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.9329 Dev= 1.43% S= 5.43 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   3.90

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     994 steps. Energy=    -387.1186528       time=       2.07
 Minus side of path:                     995 steps. Energy=    -386.2874961       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1186528 0.96050         -386.1581563 0.12934         -386.2874961   6.020   5.807   2.047  70.840
        Known (#9)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     125.77    
 decide> The unconnected minima in the chain and their distances are:
    11        5.01    10 
 

 tryconnect> 70-iteration DNEB run for minima 10_S and 11_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2425 Dev= 0.37% S= 5.36 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        153
 DNEB run yielded 1 true transition state(s) time=  11.71

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1011 steps. Energy=    -386.2874961       time=       2.11
 Minus side of path:                     981 steps. Energy=    -387.7217791       time=       2.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2874961 0.78492         -385.5025788  2.2192         -387.7217791  24.136  23.705   2.441  59.391
        Known (#11)                                             *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     229.29    
 decide> The unconnected minima in the chain and their distances are:
     2        6.12    10 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 70 RMS= 1.1798 Dev= 1.40% S= 7.23 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.29

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1017 steps. Energy=    -385.2931964       time=       2.14
 Minus side of path:                     995 steps. Energy=    -385.2626841       time=       2.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2931964  5.0626         -380.2306156  5.0321         -385.2626841  13.322   6.619   3.597  40.313
        *NEW* (Placed in 13)                                    Known (#2)
 Unconnected minimum 13 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 13 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     200.68    
 decide> The unconnected minima in the chain and their distances are:
    13        5.85     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 13_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 1.0403 Dev= 0.64% S= 6.27 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.27

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1000 steps. Energy=    -385.2931964       time=       2.09
 Minus side of path:                     992 steps. Energy=    -385.1964560       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2931964 0.48591         -384.8072899 0.38917         -385.1964560   8.314   8.199   1.677  86.484
        Known (#13)                                             *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 14 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     198.27    
 decide> The unconnected minima in the chain and their distances are:
    14        5.83     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 14_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.5718 Dev= 1.53% S= 6.25 time= 0.16
 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=  16.52
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 14 minima and 10 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     251.54    
 decide> The unconnected minima in the chain and their distances are:
    11        5.01    10 
 

 tryconnect> 385-iteration DNEB run for minima 10_S and 11_F using 11 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0138 Dev= 2.57% S= 7.12 time= 4.51
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.79

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     987 steps. Energy=    -386.2874961       time=       2.02
 Minus side of path:                    1012 steps. Energy=    -387.8018809       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2874961  2.4159         -383.8715811  3.9303         -387.8018809   6.316   5.011  22.745   6.375
        Known (#11)                                             Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -385.8079668  2.5002        -383.3077684  3.5052        -386.8129981   5.606   5.414   7.466  19.421
   6     -386.8129981 0.69984E-01    -386.7430140  1.0589        -387.8018809  10.124   9.541   1.679  86.368
  11     -387.8018809  3.9303        -383.8715811  2.4159        -386.2874961   6.316   5.011  22.745   6.375
   7     -386.2874961 0.12934        -386.1581563 0.96050        -387.1186528   6.020   5.807   2.047  70.840
   5     -387.1186528  4.8706        -382.2480505  3.0146        -385.2626841  12.088   4.668   3.230  44.895

 Number of TS in the path       =      5
 Number of cycles               =     10

 Elapsed time=                               165.67
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             61152 time=          64.22 %= 38.8
 OPTIM> # of energy+gradient+Hessian calls=       744 time=           2.82 %=  1.7
