
 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 12:36:58 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -388.7175115     RMS force=    0.8934789259E-06
 OPTIM> Final energy  =    -382.8362010     RMS force=    0.8745120097E-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=     19282.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.82     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.8083 Dev= 1.63% S= 30.00 time= 2.90
 Following    2 images are candidates for TS:    4    8  
 Converged to TS (number of iterations):         77
 Converged to TS (number of iterations):         31
 DNEB run yielded 2 true transition state(s) time=  10.91

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     945 steps. Energy=    -388.7175115       time=       3.02
 Minus side of path:                     941 steps. Energy=    -388.7877538       time=       3.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7175115 0.35773         -388.3597807 0.42797         -388.7877538   6.483   6.277   2.341  61.938
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     976 steps. Energy=    -382.8362010       time=       2.45
 Minus side of path:                    1042 steps. Energy=    -388.3561027       time=       3.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.8362010  1.4336         -381.4025743  6.9535         -388.3561027  24.503  23.795   4.867  29.794
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     157.67    
 decide> The unconnected minima in the chain and their distances are:
     4        5.40     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 4_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 7.0453 Dev= 1.89% S= 5.96 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   5.21

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     924 steps. Energy=    -388.7875488       time=       2.64
 Minus side of path:                     919 steps. Energy=    -388.7877538       time=       2.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7875488 0.16479E-01     -388.7710693 0.16685E-01     -388.7877538   0.996   0.993   3.677  39.437
        *NEW* (Placed in 5)                                     Known (#3)
 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=     171.06    
 decide> The unconnected minima in the chain and their distances are:
     4        5.55     5 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.6240 Dev= 0.27% S= 5.97 time= 0.19
 Following    1 images are candidates for TS:    1  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   5.20

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     923 steps. Energy=    -388.3575902       time=       2.72
 Minus side of path:                     897 steps. Energy=    -388.3561027       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3575902 0.17809E-01     -388.3397810 0.16322E-01     -388.3561027   1.008   1.005   3.506  41.360
        *NEW* (Placed in 6)                                     Known (#4)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     155.86    
 decide> The unconnected minima in the chain and their distances are:
     6        5.38     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2007 Dev= 0.40% S= 5.81 time= 0.19
 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=  34.21
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     158.77    
 decide> The unconnected minima in the chain and their distances are:
     6        5.41     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3396 Dev= 0.83% S= 5.87 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.51
 isnewts> transition state is the same as number        4 energy=     -388.3397810391
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     935 steps. Energy=    -388.3575902       time=       2.74
 Minus side of path:                     923 steps. Energy=    -388.3561027       time=       3.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3575902 0.17809E-01     -388.3397810 0.16322E-01     -388.3561027   1.008   1.005   3.506  41.362
        Known (#6)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     311.72    
 decide> The unconnected minima in the chain and their distances are:
     6        5.38     5 
 

 tryconnect> 420-iteration DNEB run for minima 5_S and 6_F using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0106 Dev= 4.24% S= 7.68 time= 6.48
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.63

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     957 steps. Energy=    -388.3575902       time=       2.87
 Minus side of path:                     956 steps. Energy=    -388.7875488       time=       3.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3575902  2.6126         -385.7450076  3.0425         -388.7875488   6.209   5.384  37.925   3.823
        Known (#6)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -388.7175115 0.35773        -388.3597807 0.42797        -388.7877538   6.483   6.277   2.341  61.938
   3     -388.7877538 0.16685E-01    -388.7710693 0.16479E-01    -388.7875488   0.996   0.993   3.677  39.437
   6     -388.7875488  3.0425        -385.7450076  2.6126        -388.3575902   6.209   5.384  37.925   3.823
   4     -388.3575902 0.17809E-01    -388.3397810 0.16322E-01    -388.3561027   1.008   1.005   3.506  41.360
   2     -388.3561027  6.9535        -381.4025743  1.4336        -382.8362010  24.503  23.795   4.867  29.794

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               107.40
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             28001 time=          34.78 %= 32.4
 OPTIM> # of energy+gradient+Hessian calls=       470 time=           2.19 %=  2.0
