
 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 12:48:57 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     0.1123529514    
 Double-ended search iterations= 630 RMS= 0.0446 Dev= 6.51% S= 74.05 time= 13.37
 Following    3 images are candidates for TS:    4    9   14  
 Converged to TS (number of iterations):         71
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         54
 DNEB run yielded 2 true transition state(s) time=  33.19

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1760 steps. Energy=    -382.0757114       time=       8.36
 Minus side of path:                    1034 steps. Energy=    -376.9056308       time=       3.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0757114  5.2407         -376.8349627 0.70668E-01     -376.9056308  58.711  55.881   1.811  80.070
        *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:                    1064 steps. Energy=    -382.9986292       time=       4.58
 Minus side of path:                     968 steps. Energy=    -381.9741642       time=       3.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9986292  1.0446         -381.9539938 0.20170E-01     -381.9741642  19.499  18.654   3.133  46.278
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     2930.4    
 decide> The unconnected minima in the chain and their distances are:
     2       13.60     3     4        7.47     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0760 Dev= 0.31% S= 13.98 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   8.14

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1000 steps. Energy=    -383.1759484       time=       3.42
 Minus side of path:                    1020 steps. Energy=    -382.0757114       time=       2.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.1759484  1.3976         -381.7783156 0.29740         -382.0757114  14.610  11.957   3.573  40.582
        *NEW* (Placed in 7)                                     Known (#3)
 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      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0912 Dev= 0.13% S= 7.49 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1016 steps. Energy=    -376.8434946       time=       2.58
 Minus side of path:                    1025 steps. Energy=    -376.9056308       time=       3.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.8434946 0.16235E-01     -376.8272595 0.78371E-01     -376.9056308   7.557   7.467  10.740  13.501
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1124.5    
 decide> The unconnected minima in the chain and their distances are:
     2       10.40     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 105 RMS= 0.1331 Dev= 0.63% S= 10.56 time= 0.41
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.16

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     920 steps. Energy=    -383.1759484       time=       2.70
 Minus side of path:                    1039 steps. Energy=    -386.0833114       time=       3.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.1759484 0.18827E-02     -383.1740658  2.9092         -386.0833114  11.204  10.500   5.609  25.852
        Known (#7)                                              *NEW* (Placed in 8)
 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      5 steps with      1 missing connections, weight=     658.71    
 decide> The unconnected minima in the chain and their distances are:
     2        8.70     8 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.1267 Dev= 0.15% S= 8.73 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   5.71

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     978 steps. Energy=    -385.8967771       time=       3.56
 Minus side of path:                     972 steps. Energy=    -385.2394514       time=       2.94

         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   6.935  20.909
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     247.60    
 decide> The unconnected minima in the chain and their distances are:
     9        6.28     8 
 

 tryconnect> 70-iteration DNEB run for minima 8_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.0444 Dev= 0.27% S= 6.29 time= 0.19
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   6.33

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     915 steps. Energy=    -385.8967771       time=       2.12
 Minus side of path:                     985 steps. Energy=    -386.0833114       time=       2.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8967771 0.65498E-03     -385.8961222 0.18719         -386.0833114   6.295   6.279   2.166  66.949
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -376.8434946 0.16235E-01    -376.8272595 0.78371E-01    -376.9056308   7.557   7.467  10.740  13.501
   1     -376.9056308 0.70668E-01    -376.8349627  5.2407        -382.0757114  58.711  55.881   1.811  80.070
   3     -382.0757114 0.29740        -381.7783156  1.3976        -383.1759484  14.610  11.957   3.573  40.582
   5     -383.1759484 0.18827E-02    -383.1740658  2.9092        -386.0833114  11.204  10.500   5.609  25.852
   7     -386.0833114 0.18719        -385.8961222 0.65498E-03    -385.8967771   6.295   6.279   2.166  66.949
   6     -385.8967771 0.67456        -385.2222203 0.17231E-01    -385.2394514   6.955   5.982   6.935  20.909

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

 Elapsed time=                               128.87
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             36135 time=          43.72 %= 33.9
 OPTIM> # of energy+gradient+Hessian calls=       610 time=           3.03 %=  2.4
