
 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)@comp21.ch.
                 Created on  5/28/12 at 13: 5: 8 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=    -385.3870844     RMS force=    0.9140412262E-06
 OPTIM> Final energy  =    -393.1974267     RMS force=    0.8385201297E-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=     21994.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.02     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 280 RMS= 0.4908 Dev= 0.38% S= 29.35 time= 3.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.11

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     919 steps. Energy=    -386.0389721       time=       3.29
 Minus side of path:                    1105 steps. Energy=    -393.0593149       time=       3.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0389721 0.23779         -385.8011858  7.2581         -393.0593149  21.916  20.172   3.553  40.807
        *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=     3118.5    
 decide> The unconnected minima in the chain and their distances are:
     2       12.90     4     3        9.91     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      15.51328216    
 Double-ended search iterations= 105 RMS= 0.2485 Dev= 0.56% S= 12.96 time= 0.47
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   4.07

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     844 steps. Energy=    -393.1974267       time=       2.57
 Minus side of path:                     779 steps. Energy=    -393.0593149       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.1974267 0.59074         -392.6066837 0.45263         -393.0593149  13.091  12.898   3.542  40.933
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 10.0386 Dev= 49.50% S= 18.76 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   7.68

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     960 steps. Energy=    -386.1553097       time=       2.79
 Minus side of path:                     956 steps. Energy=    -386.1368164       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1553097  1.2029         -384.9524113  1.1844         -386.1368164  10.714  10.254   3.774  38.422
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1002.4    
 decide> The unconnected minima in the chain and their distances are:
     3        1.69     5     5        9.99     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0283 Dev= 0.24% S= 1.70 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.17

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     879 steps. Energy=    -386.0389721       time=       2.08
 Minus side of path:                     923 steps. Energy=    -386.1553097       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0389721 0.72779E-02     -386.0316942 0.12362         -386.1553097   1.889   1.694   3.812  38.035
        Known (#3)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 10.2116 Dev= 51.72% S= 19.28 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.31

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     972 steps. Energy=    -386.1368164       time=       2.50
 Minus side of path:                     969 steps. Energy=    -386.1368164       time=       2.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1368164  2.6682         -383.4686107  2.6682         -386.1368164  10.269   3.054  72.412   2.002
        Known (#6)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1947.1    
 decide> The unconnected minima in the chain and their distances are:
     3        9.91     1 
 

 tryconnect> 770-iteration DNEB run for minima 1_S and 3_F using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.313774487    
 Double-ended search iterations= 770 RMS= 0.0441 Dev= 4.13% S= 12.16 time= 24.18
 Following    2 images are candidates for TS:    5   21  
 Converged to TS (number of iterations):         15
 Converged to TS (number of iterations):         13
 DNEB run yielded 2 true transition state(s) time=   8.05

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     871 steps. Energy=    -385.3870844       time=       2.22
 Minus side of path:                    1062 steps. Energy=    -386.8644418       time=       4.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.3870844  1.3985         -383.9886001  2.8758         -386.8644418  13.746  12.889   3.409  42.540
        Known (#1)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to S set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1055 steps. Energy=    -386.8644418       time=       4.18
 Minus side of path:                     854 steps. Energy=    -386.0389721       time=       2.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8644418 0.82927         -386.0351737 0.37983E-02     -386.0389721  12.370  12.082   4.631  31.313
        Known (#7)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -385.3870844  1.3985        -383.9886001  2.8758        -386.8644418  13.746  12.889   3.409  42.540
   7     -386.8644418 0.82927        -386.0351737 0.37983E-02    -386.0389721  12.370  12.082   4.631  31.313
   1     -386.0389721 0.23779        -385.8011858  7.2581        -393.0593149  21.916  20.172   3.553  40.807
   2     -393.0593149 0.45263        -392.6066837 0.59074        -393.1974267  13.091  12.898   3.542  40.933

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

 Elapsed time=                               103.66
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             39590 time=          55.01 %= 53.1
 OPTIM> # of energy+gradient+Hessian calls=       282 time=           1.38 %=  1.3
