
 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 13: 4:27 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=    -394.5922049     RMS force=    0.8795773153E-06
 OPTIM> Final energy  =    -388.4759396     RMS force=    0.9144119160E-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=     16602.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.51     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      67.04751154    
 Double-ended search iterations= 245 RMS= 1.5593 Dev= 3.57% S= 26.87 time= 2.27
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   7.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     931 steps. Energy=    -394.8959038       time=       2.06
 Minus side of path:                     887 steps. Energy=    -394.6825323       time=       1.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.8959038  1.0558         -393.8400765 0.84246         -394.6825323   4.911   4.619   9.683  14.975
        *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=     16659.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.54     4     4        1.45     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 249 RMS= 1.4750 Dev= 1.36% S= 27.15 time= 2.26
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        190
 DNEB run yielded 1 true transition state(s) time=  13.33

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     990 steps. Energy=    -390.5902368       time=       3.03
 Minus side of path:                    1015 steps. Energy=    -389.1405799       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5902368  2.3019         -388.2883667 0.85221         -389.1405799  20.547  14.244   2.345  61.827
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.2295 Dev= 2.29% S= 1.46 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.43

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     874 steps. Energy=    -394.6825323       time=       3.07
 Minus side of path:                     837 steps. Energy=    -394.5922049       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6825323 0.97054E-01     -394.5854780 0.67269E-02     -394.5922049   1.453   1.449   2.945  49.241
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     9207.8    
 decide> The unconnected minima in the chain and their distances are:
     2       19.83     6     5       11.21     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 6_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      45.38039494    
 Double-ended search iterations= 175 RMS= 1.2776 Dev= 2.59% S= 20.10 time= 1.18
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   6.35

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     963 steps. Energy=    -392.6501930       time=       2.45
 Minus side of path:                    1004 steps. Energy=    -394.5922049       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.6501930  5.3569         -387.2933107  7.2989         -394.5922049  21.292  16.166  10.037  14.446
        *NEW* (Placed in 7)                                     Known (#1)
 Unconnected minimum 7 found its way to S set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 105 RMS= 2.4731 Dev= 1.82% S= 16.82 time= 0.42
 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=  30.46
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     5707.8    
 decide> The unconnected minima in the chain and their distances are:
     2       17.87     7 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 7_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 175 RMS= 1.1035 Dev= 0.95% S= 18.27 time= 1.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   8.98

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     966 steps. Energy=    -388.4759396       time=       3.76
 Minus side of path:                    1021 steps. Energy=    -393.5152156       time=       3.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4759396 0.43787         -388.0380672  5.4771         -393.5152156  21.302  16.778   7.213  20.104
        Known (#2)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     94.848    
 decide> The unconnected minima in the chain and their distances are:
     8        4.56     7 
 

 tryconnect> 70-iteration DNEB run for minima 7_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.1440 Dev= 0.44% S= 4.60 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.22

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     978 steps. Energy=    -393.5152156       time=       2.55
 Minus side of path:                     925 steps. Energy=    -392.6501930       time=       2.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.5152156  1.0177         -392.4975239 0.15267         -392.6501930   4.944   4.561   4.332  33.470
        Known (#8)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -394.5922049  7.2989        -387.2933107  5.3569        -392.6501930  21.292  16.166  10.037  14.446
   6     -392.6501930 0.15267        -392.4975239  1.0177        -393.5152156   4.944   4.561   4.332  33.470
   5     -393.5152156  5.4771        -388.0380672 0.43787        -388.4759396  21.302  16.778   7.213  20.104

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               115.48
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             25555 time=          33.80 %= 29.3
 OPTIM> # of energy+gradient+Hessian calls=       691 time=           3.54 %=  3.1
