
 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)@comp25.ch.
                 Created on  5/28/12 at 12:59:24 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=    -392.4501307     RMS force=    0.9782326442E-06
 OPTIM> Final energy  =    -388.4290083     RMS force=    0.8748875964E-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=     18321.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.36     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 245 RMS= 0.2343 Dev= 0.86% S= 27.66 time= 2.61
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=  10.95

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     992 steps. Energy=    -386.8836942       time=       3.68
 Minus side of path:                    1017 steps. Energy=    -392.2873836       time=       4.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8836942  1.8198         -385.0639149  7.2235         -392.2873836  29.948  25.598   1.968  73.693
        *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      3 steps with      2 missing connections, weight=     6983.3    
 decide> The unconnected minima in the chain and their distances are:
     2       19.11     3     4        2.04     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0446 Dev= 0.12% S= 19.41 time= 1.29
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   7.16

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1123 steps. Energy=    -388.4290083       time=       3.67
 Minus side of path:                     959 steps. Energy=    -386.8836942       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4290083  1.7152         -386.7137670 0.16993         -386.8836942  21.694  19.122   5.376  26.972
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0753 Dev= 0.30% S= 2.05 time= 0.21
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     901 steps. Energy=    -392.4501307       time=       2.57
 Minus side of path:                     912 steps. Energy=    -392.4339967       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4501307 0.71047E-01     -392.3790833 0.54913E-01     -392.4339967   1.280   1.266   4.727  30.676
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1.5327    
 decide> The unconnected minima in the chain and their distances are:
     4        1.15     5 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 5_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0189 Dev= 0.18% S= 1.17 time= 0.21
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   7.44
 isnewts> transition state is the same as number        3 energy=     -392.3790832980
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     931 steps. Energy=    -392.4501307       time=       3.49
 Minus side of path:                     936 steps. Energy=    -392.4339967       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4501307 0.71047E-01     -392.3790833 0.54913E-01     -392.4339967   1.280   1.266   4.727  30.674
        Known (#1)                                              Known (#5)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     3.0654    
 decide> The unconnected minima in the chain and their distances are:
     4        1.15     5 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 5_S using 2 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1894 Dev= 0.14% S= 1.17 time= 0.22
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  29.27
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     4.5980    
 decide> The unconnected minima in the chain and their distances are:
     4        1.15     5 
 

 tryconnect> 140-iteration DNEB run for minima 4_F and 5_S using 4 images  (DNEB attempt #3)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.0306 Dev= 0.78% S= 1.23 time= 0.82
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.44

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     924 steps. Energy=    -392.4339967       time=       2.84
 Minus side of path:                     866 steps. Energy=    -392.2873836       time=       2.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4339967 0.14709         -392.2869095 0.47412E-03     -392.2873836   1.155   1.153   4.241  34.186
        Known (#5)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -392.4501307 0.71047E-01    -392.3790833 0.54913E-01    -392.4339967   1.280   1.266   4.727  30.676
   5     -392.4339967 0.14709        -392.2869095 0.47412E-03    -392.2873836   1.155   1.153   4.241  34.186
   1     -392.2873836  7.2235        -385.0639149  1.8198        -386.8836942  29.948  25.598   1.968  73.693
   2     -386.8836942 0.16993        -386.7137670  1.7152        -388.4290083  21.694  19.122   5.376  26.972

 Number of TS in the path       =      4
 Number of cycles               =      5

 Elapsed time=                               102.19
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             20625 time=          29.80 %= 29.2
 OPTIM> # of energy+gradient+Hessian calls=       538 time=           2.99 %=  2.9
