
 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)@comp27.ch.
                 Created on  5/28/12 at 12:54:29 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=    -376.8434946     RMS force=    0.9352800497E-06
 OPTIM> Final energy  =    -385.2394514     RMS force=    0.9243098185E-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=    0.21942E+06
 decide> The unconnected minima in the chain and their distances are:
     2       60.31     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 2_F using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      24.06619234    
 Double-ended search iterations= 630 RMS= 0.1927 Dev= 0.48% S= 61.71 time= 13.36
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        190
 DNEB run yielded 1 true transition state(s) time=  19.33

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     968 steps. Energy=    -381.9741642       time=       3.36
 Minus side of path:                    1041 steps. Energy=    -382.9986292       time=       4.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.9741642 0.20170E-01     -381.9539938  1.0446         -382.9986292  19.499  18.654   3.132  46.297
        *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=     74631.    
 decide> The unconnected minima in the chain and their distances are:
     2       17.92     4     3       40.99     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 175 RMS= 0.1205 Dev= 0.66% S= 18.08 time= 1.24
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.53

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1038 steps. Energy=    -385.2394514       time=       3.05
 Minus side of path:                     954 steps. Energy=    -382.9986292       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2394514  2.3023         -382.9371072 0.61522E-01     -382.9986292  18.317  17.924   3.563  40.692
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 420-iteration DNEB run for minima 1_S and 3_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 420 RMS= 0.1566 Dev= 0.43% S= 42.23 time= 5.78
 Following    1 images are candidates for TS:    6  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  25.77
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.13776E+06
 decide> The unconnected minima in the chain and their distances are:
     3       40.99     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 805 RMS= 0.0596 Dev= 2.15% S= 46.98 time= 20.70
 Following    1 images are candidates for TS:   10  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  18.28
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.16022E+06
 decide> The unconnected minima in the chain and their distances are:
     4       54.31     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 4_F using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 560 RMS= 0.4139 Dev= 0.53% S= 55.90 time= 10.44
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        184
 DNEB run yielded 1 true transition state(s) time=  13.90

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1271 steps. Energy=    -386.0833114       time=       3.80
 Minus side of path:                    1081 steps. Energy=    -381.6649192       time=       2.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0833114  5.0364         -381.0468922 0.61803         -381.6649192  35.165  24.490   3.395  42.715
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=    0.13091E+06
 decide> The unconnected minima in the chain and their distances are:
     2        8.70     5     6       50.69     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 0.1537 Dev= 0.41% S= 8.72 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     988 steps. Energy=    -385.8967771       time=       2.79
 Minus side of path:                     992 steps. Energy=    -385.2394514       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8967771 0.67456         -385.2222203 0.17231E-01     -385.2394514   6.955   5.982   6.933  20.913
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 525-iteration DNEB run for minima 1_S and 6_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 525 RMS= 0.0634 Dev= 1.22% S= 51.57 time= 9.20
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         98
 DNEB run yielded 1 true transition state(s) time=   7.37

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1033 steps. Energy=    -376.8434946       time=       2.64
 Minus side of path:                    2357 steps. Energy=    -386.6404421       time=      15.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.8434946 0.81899E-01     -376.7615954  9.8788         -386.6404421  70.801  67.529   1.974  73.465
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     30553.    
 decide> The unconnected minima in the chain and their distances are:
     7        6.28     5     6       31.18     8 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0627 Dev= 0.44% S= 6.29 time= 0.19
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  48.14

 tryconnect> 315-iteration DNEB run for minima 6_U and 8_S using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 315 RMS= 0.2979 Dev= 0.89% S= 31.78 time= 3.62
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   8.03

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     959 steps. Energy=    -381.6649192       time=       2.37
 Minus side of path:                    1102 steps. Energy=    -386.6906328       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.6649192 0.21686         -381.4480611  5.2426         -386.6906328  32.810  29.416   1.947  74.463
        Known (#6)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     753.64    
 decide> The unconnected minima in the chain and their distances are:
     7        6.28     5     9        6.37     8 
 

 tryconnect> 490-iteration DNEB run for minima 5_U and 7_F using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 490 RMS= 0.0055 Dev= 1.06% S= 6.43 time= 9.20
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.71

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     987 steps. Energy=    -386.0833114       time=       2.40
 Minus side of path:                     922 steps. Energy=    -385.8967771       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0833114 0.18719         -385.8961222 0.65498E-03     -385.8967771   6.295   6.279   2.166  66.948
        Known (#5)                                              Known (#7)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0393 Dev= 0.19% S= 6.38 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.16

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     940 steps. Energy=    -386.6906328       time=       2.65
 Minus side of path:                     881 steps. Energy=    -386.6404421       time=       2.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.6906328 0.53792E-01     -386.6368411 0.36010E-02     -386.6404421   6.601   6.370  11.296  12.836
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -376.8434946 0.81899E-01    -376.7615954  9.8788        -386.6404421  70.801  67.529   1.974  73.465
   8     -386.6404421 0.36010E-02    -386.6368411 0.53792E-01    -386.6906328   6.601   6.370  11.296  12.836
   6     -386.6906328  5.2426        -381.4480611 0.21686        -381.6649192  32.810  29.416   1.947  74.463
   3     -381.6649192 0.61803        -381.0468922  5.0364        -386.0833114  35.165  24.490   3.395  42.715
   7     -386.0833114 0.18719        -385.8961222 0.65498E-03    -385.8967771   6.295   6.279   2.166  66.948
   4     -385.8967771 0.67456        -385.2222203 0.17231E-01    -385.2394514   6.955   5.982   6.933  20.913

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               289.62
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             96894 time=         113.17 %= 39.1
 OPTIM> # of energy+gradient+Hessian calls=      1394 time=           6.44 %=  2.2
