
 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)@comp28.ch.
                 Created on  5/28/12 at 12:53:32 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=    -381.4721359     RMS force=    0.9165938109E-06
 OPTIM> Final energy  =    -382.2034186     RMS force=    0.9976630485E-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=     45557.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.72     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3623494974    
 Double-ended search iterations= 350 RMS= 0.0861 Dev= 0.58% S= 40.81 time= 3.85
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  18.82
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     91114.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.72     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 805 RMS= 0.0941 Dev= 4.28% S= 45.23 time= 20.44
 Following    2 images are candidates for TS:    8   13  
 Converged to TS (number of iterations):         83
 Converged to TS (number of iterations):         77
 DNEB run yielded 2 true transition state(s) time=  15.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1123 steps. Energy=    -380.0234371       time=       3.41
 Minus side of path:                    1027 steps. Energy=    -381.4282510       time=       3.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.0234371 0.66870         -379.3547362  2.0735         -381.4282510  41.497  39.475   1.809  80.156
        *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:                    1004 steps. Energy=    -382.1663989       time=       3.77
 Minus side of path:                    1022 steps. Energy=    -382.1851430       time=       3.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1663989 0.14303E-01     -382.1520962 0.33047E-01     -382.1851430   1.745   1.740   2.843  51.010
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     22811.    
 decide> The unconnected minima in the chain and their distances are:
     2        1.09     5     6       28.17     3     4        7.66     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0114 Dev= 0.06% S= 1.09 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.93

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     993 steps. Energy=    -382.1663989       time=       2.97
 Minus side of path:                    1022 steps. Energy=    -382.2034186       time=       3.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1663989 0.23477E-01     -382.1429222 0.60496E-01     -382.2034186   1.105   1.090  16.194   8.954
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 3_U and 6_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 280 RMS= 0.0619 Dev= 1.20% S= 31.06 time= 2.53
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   6.36

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1021 steps. Energy=    -382.1663989       time=       3.03
 Minus side of path:                    1021 steps. Energy=    -380.7879935       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1663989  3.7501         -378.4162786  2.3717         -380.7879935  18.723  10.387  22.711   6.385
        Known (#5)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 4.2610 Dev= 0.07% S= 7.69 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   4.53

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1026 steps. Energy=    -381.4742424       time=       3.04
 Minus side of path:                     997 steps. Energy=    -381.4721359       time=       3.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4742424 0.19943E-01     -381.4542995 0.17836E-01     -381.4721359   1.894   1.891   2.529  57.324
        *NEW* (Placed in 8)                                     Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     22463.    
 decide> The unconnected minima in the chain and their distances are:
     7       28.06     3     4        7.21     8 
 

 tryconnect> 280-iteration DNEB run for minima 3_U and 7_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0238 Dev= 0.08% S= 28.39 time= 2.49
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.73

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1031 steps. Energy=    -380.7727545       time=       3.02
 Minus side of path:                     977 steps. Energy=    -380.0234371       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545 0.80237         -379.9703813 0.53056E-01     -380.0234371  27.258  27.024   1.910  75.910
        *NEW* (Placed in 9)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0186 Dev= 0.00% S= 7.21 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   6.56

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     989 steps. Energy=    -381.4742424       time=       3.73
 Minus side of path:                     973 steps. Energy=    -381.4282510       time=       3.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4742424 0.48669E-01     -381.4255732 0.26777E-02     -381.4282510   7.250   7.206   2.065  70.209
        Known (#8)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     3.9007    
 decide> The unconnected minima in the chain and their distances are:
     7        1.57     9 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0759 Dev= 0.01% S= 1.58 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.35

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1001 steps. Energy=    -380.7727545       time=       2.19
 Minus side of path:                    1016 steps. Energy=    -380.7879935       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545 0.10401E-01     -380.7623536 0.25640E-01     -380.7879935   1.577   1.574   2.911  49.815
        Known (#9)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -381.4721359 0.17836E-01    -381.4542995 0.19943E-01    -381.4742424   1.894   1.891   2.529  57.324
   7     -381.4742424 0.48669E-01    -381.4255732 0.26777E-02    -381.4282510   7.250   7.206   2.065  70.209
   1     -381.4282510  2.0735        -379.3547362 0.66870        -380.0234371  41.497  39.475   1.809  80.156
   6     -380.0234371 0.53056E-01    -379.9703813 0.80237        -380.7727545  27.258  27.024   1.910  75.910
   8     -380.7727545 0.10401E-01    -380.7623536 0.25640E-01    -380.7879935   1.577   1.574   2.911  49.815
   4     -380.7879935  2.3717        -378.4162786  3.7501        -382.1663989  18.723  10.387  22.711   6.385
   3     -382.1663989 0.23477E-01    -382.1429222 0.60496E-01    -382.2034186   1.105   1.090  16.194   8.954

 Number of TS in the path       =      7
 Number of cycles               =      5

 Elapsed time=                               143.22
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             53628 time=          57.56 %= 40.2
 OPTIM> # of energy+gradient+Hessian calls=       580 time=           2.62 %=  1.8
