
 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)@comp33.ch.
                 Created on  5/28/12 at 13: 3:45 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=    -389.2335056     RMS force=    0.9313438436E-06
 OPTIM> Final energy  =    -389.1046918     RMS force=    0.8739094660E-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=    0.12925E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.56     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 525 RMS= 0.0936 Dev= 4.74% S= 65.85 time= 11.00
 Following    2 images are candidates for TS:    7   13  
 Converged to TS (number of iterations):         36
 Converged to TS (number of iterations):        238
 DNEB run yielded 2 true transition state(s) time=  35.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     916 steps. Energy=    -388.4519192       time=       2.16
 Minus side of path:                     867 steps. Energy=    -388.3597135       time=       1.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4519192 0.10894         -388.3429796 0.16734E-01     -388.3597135   0.984   0.981  39.266   3.693
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     886 steps. Energy=    -390.8389794       time=       2.19
 Minus side of path:                    1090 steps. Energy=    -394.7569784       time=       3.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.8389794  3.3186         -387.5203838  7.2366         -394.7569784  23.729  16.448  14.430  10.049
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     71038.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.70     4     3       29.45     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 4_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 350 RMS= 0.1409 Dev= 2.83% S= 41.79 time= 5.06
 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=  20.59

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.7681 Dev= 0.23% S= 31.08 time= 3.21
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   6.21

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1112 steps. Energy=    -389.2335056       time=       4.23
 Minus side of path:                    1032 steps. Energy=    -388.4519192       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2335056  2.9859         -386.2475829  2.2043         -388.4519192  32.790  29.514   4.086  35.484
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     46405.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.94     3 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 3_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3994903209    
 Double-ended search iterations= 350 RMS= 0.1147 Dev= 2.72% S= 42.23 time= 4.80
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   6.71

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     953 steps. Energy=    -387.4362607       time=       3.98
 Minus side of path:                     944 steps. Energy=    -389.1046918       time=       3.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4362607  3.9773         -383.4589420  5.6457         -389.1046918  18.744  16.147   6.797  21.334
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     28239.    
 decide> The unconnected minima in the chain and their distances are:
     7       30.45     4 
 

 tryconnect> 315-iteration DNEB run for minima 4_S and 7_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0415 Dev= 1.44% S= 32.51 time= 4.12
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   7.88

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     945 steps. Energy=    -388.4040839       time=       3.82
 Minus side of path:                     900 steps. Energy=    -388.2930478       time=       3.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4040839 0.43554         -387.9685469 0.32450         -388.2930478  10.733  10.336   2.384  60.823
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     28887.    
 decide> The unconnected minima in the chain and their distances are:
     7       30.68     3 
 

 tryconnect> 315-iteration DNEB run for minima 3_S and 7_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0465 Dev= 0.86% S= 32.72 time= 4.06
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   7.66
 isnewts> transition state is the same as number        5 energy=     -387.9685469481
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     941 steps. Energy=    -388.4040839       time=       3.09
 Minus side of path:                     913 steps. Energy=    -388.2930478       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4040839 0.43554         -387.9685469 0.32450         -388.2930478  10.733  10.336   2.384  60.820
        Known (#8)                                              Known (#9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     34494.    
 decide> The unconnected minima in the chain and their distances are:
     7        6.73     9     9       32.46     4 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0770 Dev= 0.03% S= 6.77 time= 0.28
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.73

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     901 steps. Energy=    -387.4362607       time=       2.95
 Minus side of path:                     934 steps. Energy=    -388.2930478       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4362607 0.79515E-02     -387.4283093 0.86474         -388.2930478   6.798   6.734  14.837   9.773
        Known (#7)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 4_S and 9_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0787 Dev= 1.78% S= 35.06 time= 4.12
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.53

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     886 steps. Energy=    -388.2386015       time=       2.42
 Minus side of path:                    1006 steps. Energy=    -388.5796269       time=       4.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2386015 0.87707         -387.3615291  1.2181         -388.5796269  14.127  13.006   2.084  69.584
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     9151.4    
 decide> The unconnected minima in the chain and their distances are:
     9       14.04    11    10       18.55     4 
 

 tryconnect> 140-iteration DNEB run for minima 9_F and 11_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0739 Dev= 0.04% S= 14.13 time= 0.90
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   5.92
 isnewts> transition state is the same as number        5 energy=     -387.9685469479
 tryconnect> Will not repeat search for TS      1 same as TS      5

 tryconnect> 175-iteration DNEB run for minima 4_S and 10_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0297 Dev= 0.04% S= 18.67 time= 1.27
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.10

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1050 steps. Energy=    -388.2386015       time=       2.84
 Minus side of path:                     925 steps. Energy=    -388.4519192       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2386015 0.70317         -387.5354327 0.91649         -388.4519192  21.724  18.872   3.275  44.273
        Known (#10)                                             Known (#3)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3186.5    
 decide> The unconnected minima in the chain and their distances are:
     7       14.72    11 
 

 tryconnect> 140-iteration DNEB run for minima 7_F and 11_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0731 Dev= 0.11% S= 14.94 time= 0.86
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   4.92
 isnewts> transition state is the same as number        7 energy=     -387.4283092578
 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:                     890 steps. Energy=    -387.4362607       time=       2.19
 Minus side of path:                     932 steps. Energy=    -388.2930478       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4362607 0.79515E-02     -387.4283093 0.86474         -388.2930478   6.798   6.734  14.817   9.786
        Known (#7)                                              Known (#9)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     4399.5    
 decide> The unconnected minima in the chain and their distances are:
     8       16.39    11 
 

 tryconnect> 140-iteration DNEB run for minima 8_F and 11_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.3991 Dev= 0.04% S= 16.46 time= 0.86
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   5.06

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     921 steps. Energy=    -388.6809028       time=       3.20
 Minus side of path:                     916 steps. Energy=    -388.4040839       time=       3.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6809028 0.28912         -388.3917789 0.12305E-01     -388.4040839   3.643   3.560   3.024  47.951
        *NEW* (Placed in 12)                                    Known (#8)
 Unconnected minimum 12 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     3791.1    
 decide> The unconnected minima in the chain and their distances are:
    12       15.59    11 
 

 tryconnect> 140-iteration DNEB run for minima 11_S and 12_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0391 Dev= 0.01% S= 15.64 time= 0.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   7.09

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     901 steps. Energy=    -388.5796269       time=       2.17
 Minus side of path:                     949 steps. Energy=    -388.6809028       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5796269 0.42288E-01     -388.5373394 0.14356         -388.6809028  15.726  15.593   2.038  71.140
        Known (#11)                                             Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -389.2335056  2.9859        -386.2475829  2.2043        -388.4519192  32.790  29.514   4.086  35.484
   9     -388.4519192 0.91649        -387.5354327 0.70317        -388.2386015  21.724  18.872   3.275  44.273
   8     -388.2386015 0.87707        -387.3615291  1.2181        -388.5796269  14.127  13.006   2.084  69.584
  12     -388.5796269 0.42288E-01    -388.5373394 0.14356        -388.6809028  15.726  15.593   2.038  71.140
  11     -388.6809028 0.28912        -388.3917789 0.12305E-01    -388.4040839   3.643   3.560   3.024  47.951
   5     -388.4040839 0.43554        -387.9685469 0.32450        -388.2930478  10.733  10.336   2.384  60.823
   7     -388.2930478 0.86474        -387.4283093 0.79515E-02    -387.4362607   6.798   6.734  14.837   9.773
   4     -387.4362607  3.9773        -383.4589420  5.6457        -389.1046918  18.744  16.147   6.797  21.334

 Number of TS in the path       =      8
 Number of cycles               =     10

 Elapsed time=                               236.47
 OPTIM> # of energy calls=                        186 time=           0.25 %=  0.1
 OPTIM> # of energy+gradient calls=             67599 time=          93.00 %= 39.3
 OPTIM> # of energy+gradient+Hessian calls=      1078 time=           5.53 %=  2.3
