
 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)@comp21.ch.
                 Created on  5/28/12 at 13: 3:38 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=    -386.1053788     RMS force=    0.9501329568E-06
 OPTIM> Final energy  =    -396.8219334     RMS force=    0.7851346602E-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=     52419.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.43     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.2311 Dev= 2.69% S= 46.30 time= 5.95
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=   7.72

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     942 steps. Energy=    -387.2405770       time=       2.23
 Minus side of path:                     935 steps. Energy=    -388.5631391       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.2405770 0.25436         -386.9862173  1.5769         -388.5631391   8.130   7.123   5.131  28.259
        *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      2 steps with      2 missing connections, weight=     46837.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.74     3     3       35.81     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.6577 Dev= 0.18% S= 10.70 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   5.02
 isnewts> transition state is the same as number        1 energy=     -386.9862172719
 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:                     954 steps. Energy=    -387.2405770       time=       2.27
 Minus side of path:                     949 steps. Energy=    -388.5631391       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.2405770 0.25436         -386.9862173  1.5769         -388.5631391   8.130   7.123   5.131  28.261
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 3_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0709 Dev= 1.12% S= 40.94 time= 4.78
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        116
 DNEB run yielded 1 true transition state(s) time=   8.18

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1140 steps. Energy=    -388.4421440       time=       3.06
 Minus side of path:                    1292 steps. Energy=    -389.9957168       time=       3.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4421440  2.2473         -386.1948290  3.8009         -389.9957168  29.221  21.042   7.070  20.510
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     54511.    
 decide> The unconnected minima in the chain and their distances are:
     2       10.05     4     4       37.68     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2674 Dev= 1.28% S= 10.66 time= 0.51
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    3  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=   6.92

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     925 steps. Energy=    -397.1770852       time=       2.17
 Minus side of path:                     963 steps. Energy=    -396.8219334       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.1770852  2.1269         -395.0502238  1.7717         -396.8219334  18.142  17.573   3.641  39.829
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 4_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0994 Dev= 3.32% S= 45.02 time= 5.77
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   6.10

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     961 steps. Energy=    -388.3073475       time=       2.28
 Minus side of path:                     921 steps. Energy=    -387.2405770       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3073475  1.3705         -386.9368205 0.30376         -387.2405770   8.507   7.991   3.939  36.808
        *NEW* (Placed in 8)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     62110.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.74     3     8       39.21     1 
 

 tryconnect> 770-iteration DNEB run for minima 2_F and 3_U using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 770 RMS= 0.0166 Dev= 5.16% S= 19.68 time= 23.97
 Following    2 images are candidates for TS:   13   21  
 Converged to TS (number of iterations):         20
 Converged to TS (number of iterations):         13
 DNEB run yielded 2 true transition state(s) time=   7.90
 isnewts> transition state is the same as number        1 energy=     -386.9862172717
 tryconnect> Will not repeat search for TS      2 same as TS      1

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     915 steps. Energy=    -388.5631391       time=       3.20
 Minus side of path:                     953 steps. Energy=    -396.8219334       time=       3.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5631391 0.19154         -388.3715992  8.4503         -396.8219334  12.238  10.053   5.446  26.625
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 8_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0636 Dev= 1.73% S= 44.37 time= 5.91
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   6.02

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     973 steps. Energy=    -385.9147220       time=       3.06
 Minus side of path:                     977 steps. Energy=    -386.1053788       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9147220 0.19669         -385.7180324 0.38735         -386.1053788  17.689  16.887   3.995  36.293
        *NEW* (Placed in 9)                                     Known (#1)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     17687.    
 decide> The unconnected minima in the chain and their distances are:
     3       26.05     9 
 

 tryconnect> 245-iteration DNEB run for minima 3_F and 9_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.9826 Dev= 0.34% S= 27.29 time= 2.44
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.39
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     20062.    
 decide> The unconnected minima in the chain and their distances are:
     8        1.29     5     6       27.17     9 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0515 Dev= 0.19% S= 1.30 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   3.03

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     875 steps. Energy=    -388.4421440       time=       2.72
 Minus side of path:                     877 steps. Energy=    -388.3073475       time=       2.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4421440 0.15003         -388.2921139 0.15234E-01     -388.3073475   1.298   1.290   5.244  27.649
        Known (#5)                                              Known (#8)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 6_F and 9_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0616 Dev= 0.56% S= 28.42 time= 3.14
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   4.64

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     910 steps. Energy=    -385.9147220       time=       2.66
 Minus side of path:                    1216 steps. Energy=    -390.3044736       time=       4.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9147220 0.20461E-02     -385.9126758  4.3918         -390.3044736  29.905  29.576   1.926  75.289
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     2854.8    
 decide> The unconnected minima in the chain and their distances are:
     6       14.19    10 
 

 tryconnect> 140-iteration DNEB run for minima 6_F and 10_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0554 Dev= 0.10% S= 14.35 time= 0.88
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   5.58

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     976 steps. Energy=    -389.9957168       time=       3.69
 Minus side of path:                    1011 steps. Energy=    -390.3044736       time=       3.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.9957168 0.82905         -389.1666716  1.1378         -390.3044736  16.354  14.187   3.284  44.159
        Known (#6)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -386.1053788 0.38735        -385.7180324 0.19669        -385.9147220  17.689  16.887   3.995  36.293
   9     -385.9147220 0.20461E-02    -385.9126758  4.3918        -390.3044736  29.905  29.576   1.926  75.289
  10     -390.3044736  1.1378        -389.1666716 0.82905        -389.9957168  16.354  14.187   3.284  44.159
   3     -389.9957168  3.8009        -386.1948290  2.2473        -388.4421440  29.221  21.042   7.070  20.510
   8     -388.4421440 0.15003        -388.2921139 0.15234E-01    -388.3073475   1.298   1.290   5.244  27.649
   5     -388.3073475  1.3705        -386.9368205 0.30376        -387.2405770   8.507   7.991   3.939  36.808
   1     -387.2405770 0.25436        -386.9862173  1.5769        -388.5631391   8.130   7.123   5.131  28.259
   6     -388.5631391 0.19154        -388.3715992  8.4503        -396.8219334  12.238  10.053   5.446  26.625

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

 Elapsed time=                               192.88
 OPTIM> # of energy calls=                        182 time=           0.24 %=  0.1
 OPTIM> # of energy+gradient calls=             70299 time=          94.75 %= 49.1
 OPTIM> # of energy+gradient+Hessian calls=       888 time=           3.93 %=  2.0
