
 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)@comp33.ch.
                 Created on  5/28/12 at 12:51:50 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=    -394.5890829     RMS force=    0.8668942108E-06
 OPTIM> Final energy  =    -401.3454376     RMS force=    0.9309026839E-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=     15554.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.96     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1133 Dev= 0.98% S= 27.85 time= 2.63
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.45

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     979 steps. Energy=    -394.5890829       time=       3.63
 Minus side of path:                     918 steps. Energy=    -393.5316147       time=       3.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.5890829  3.1498         -391.4392777  2.0923         -393.5316147   9.757   9.002  22.679   6.394
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     8374.1    
 decide> The unconnected minima in the chain and their distances are:
     2       20.31     3 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 3_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2139 Dev= 0.88% S= 22.65 time= 1.96
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):         79
 Converged to TS (number of iterations):         85
 DNEB run yielded 2 true transition state(s) time=  14.91

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     990 steps. Energy=    -401.3454376       time=       2.54
 Minus side of path:                     868 steps. Energy=    -396.6732149       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.3454376  4.6753         -396.6701467 0.30682E-02     -396.6732149  17.800  17.580   4.486  32.322
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1095 steps. Energy=    -396.2688547       time=       3.21
 Minus side of path:                     920 steps. Energy=    -393.5316147       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.2688547  3.4582         -392.8106089 0.72101         -393.5316147  24.721  20.121   4.735  30.623
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     374.52    
 decide> The unconnected minima in the chain and their distances are:
     4        7.21     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 4_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4707 Dev= 1.05% S= 8.06 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   8.66

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     862 steps. Energy=    -393.5316147       time=       2.53
 Minus side of path:                     807 steps. Energy=    -393.0788172       time=       2.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.5316147 0.45666         -393.0749519 0.38653E-02     -393.0788172  11.765  11.663   2.500  58.001
        Known (#3)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     650.74    
 decide> The unconnected minima in the chain and their distances are:
     2        8.67     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7507 Dev= 0.87% S= 9.44 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   5.07

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     682 steps. Energy=    -396.0162911       time=       2.01
 Minus side of path:                     781 steps. Energy=    -396.2688547       time=       1.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.0162911 0.76498E-02     -396.0086413 0.26021         -396.2688547   2.413   2.375   8.375  17.313
        *NEW* (Placed in 7)                                     Known (#5)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     565.90    
 decide> The unconnected minima in the chain and their distances are:
     2        8.27     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4307 Dev= 0.79% S= 8.98 time= 0.22
 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=  25.80
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     749.03    
 decide> The unconnected minima in the chain and their distances are:
     4        7.21     3 
 

 tryconnect> 560-iteration DNEB run for minima 3_S and 4_F using 16 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      21.82874588    
 Double-ended search iterations= 560 RMS= 0.1556 Dev= 3.78% S= 9.72 time= 14.10
 Following    2 images are candidates for TS:    2   11  
 Converged to TS (number of iterations):         21
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=   9.58

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     904 steps. Energy=    -393.5316147       time=       4.13
 Minus side of path:                     921 steps. Energy=    -393.3354574       time=       4.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.5316147  1.6432         -391.8883787  1.4471         -393.3354574   4.011   2.159  21.259   6.821
        Known (#3)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     936 steps. Energy=    -396.6732149       time=       4.30
 Minus side of path:                     928 steps. Energy=    -396.9896486       time=       2.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6732149  4.7101         -391.9630805  5.0266         -396.9896486   6.543   5.671  36.860   3.934
        Known (#4)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     68.978    
 decide> The unconnected minima in the chain and their distances are:
     9        4.10     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3354 Dev= 0.58% S= 4.47 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   5.40

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1130 steps. Energy=    -395.7807786       time=       4.54
 Minus side of path:                     883 steps. Energy=    -393.5316147       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.7807786  4.2886         -391.4921539  2.0395         -393.5316147  17.371  16.588   3.032  47.830
        *NEW* (Placed in 10)                                    Known (#3)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     92.231    
 decide> The unconnected minima in the chain and their distances are:
     9        4.52     8 
 

 tryconnect> 70-iteration DNEB run for minima 8_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1816 Dev= 0.40% S= 4.67 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.62

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     931 steps. Energy=    -396.9896486       time=       2.89
 Minus side of path:                     875 steps. Energy=    -393.3354574       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.9896486  4.1481         -392.8415746 0.49388         -393.3354574   5.230   4.519  11.932  12.152
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -394.5890829  3.1498        -391.4392777  2.0923        -393.5316147   9.757   9.002  22.679   6.394
   6     -393.5316147  1.6432        -391.8883787  1.4471        -393.3354574   4.011   2.159  21.259   6.821
   9     -393.3354574 0.49388        -392.8415746  4.1481        -396.9896486   5.230   4.519  11.932  12.152
   7     -396.9896486  5.0266        -391.9630805  4.7101        -396.6732149   6.543   5.671  36.860   3.934
   2     -396.6732149 0.30682E-02    -396.6701467  4.6753        -401.3454376  17.800  17.580   4.486  32.322

 Number of TS in the path       =      5
 Number of cycles               =      8

 Elapsed time=                               152.22
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             39322 time=          58.17 %= 38.2
 OPTIM> # of energy+gradient+Hessian calls=       637 time=           3.65 %=  2.4
