
 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)@comp35.ch.
                 Created on  5/28/12 at 12:49:22 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=    -389.2335056     RMS force=    0.9313438436E-06
 OPTIM> Final energy  =    -389.1046918     RMS force=    0.8739094660E-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=    0.12925E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.56     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1580918855    
 Double-ended search iterations= 525 RMS= 0.0888 Dev= 3.58% S= 65.84 time= 10.93
 Following    2 images are candidates for TS:    7   13  
 Converged to TS (number of iterations):        116
 Converged to TS (number of iterations):         31
 DNEB run yielded 2 true transition state(s) time=  13.35

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1115 steps. Energy=    -389.2335056       time=       3.35
 Minus side of path:                    1033 steps. Energy=    -388.4519192       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2335056  2.9859         -386.2475829  2.2043         -388.4519192  32.790  29.513   4.087  35.482
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     967 steps. Energy=    -385.4005012       time=       2.35
 Minus side of path:                     974 steps. Energy=    -388.6809028       time=       2.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4005012 0.50217         -384.8983285  3.7826         -388.6809028  20.588  19.381   2.513  57.696
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     29678.    
 decide> The unconnected minima in the chain and their distances are:
     2        7.82     4     5       30.79     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.4570 Dev= 0.10% S= 7.99 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   5.12

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     948 steps. Energy=    -385.4120596       time=       3.24
 Minus side of path:                    1059 steps. Energy=    -390.5554047       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4120596 0.47753         -384.9345330  5.6209         -390.5554047  13.458  11.904   7.852  18.467
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 3_S and 5_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0356 Dev= 0.92% S= 32.41 time= 3.89
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=   6.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1058 steps. Energy=    -388.2386015       time=       2.80
 Minus side of path:                     923 steps. Energy=    -388.4519192       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2386015 0.70317         -387.5354327 0.91649         -388.4519192  21.724  18.872   3.275  44.274
        *NEW* (Placed in 8)                                     Known (#3)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     18616.    
 decide> The unconnected minima in the chain and their distances are:
     2        8.10     6     6        1.53     4     5       26.25     8 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2419 Dev= 0.83% S= 8.24 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.08
 isnewts> transition state is the same as number        3 energy=     -384.9345330391
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1046 steps. Energy=    -390.5554047       time=       2.82
 Minus side of path:                     933 steps. Energy=    -385.4120596       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5554047  5.6209         -384.9345330 0.47753         -385.4120596  13.459  11.904   7.859  18.450
        Known (#7)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.2516 Dev= 0.12% S= 1.53 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.16

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     924 steps. Energy=    -385.4005012       time=       3.34
 Minus side of path:                     913 steps. Energy=    -385.4120596       time=       2.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4005012 0.24639E-01     -385.3758621 0.36197E-01     -385.4120596   1.536   1.526   2.960  48.991
        Known (#4)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 5_U and 8_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0435 Dev= 0.38% S= 27.00 time= 2.45
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.19

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     873 steps. Energy=    -388.2386015       time=       2.11
 Minus side of path:                    1005 steps. Energy=    -388.5796269       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2386015 0.87707         -387.3615291  1.2181         -388.5796269  14.127  13.006   2.084  69.582
        Known (#8)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     4746.4    
 decide> The unconnected minima in the chain and their distances are:
     2        7.82     4     5       15.59     9 
 

 tryconnect> 595-iteration DNEB run for minima 2_F and 4_U using 17 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 595 RMS= 0.0210 Dev= 7.46% S= 12.11 time= 13.61
 Following    2 images are candidates for TS:    2   15  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         14
 DNEB run yielded 2 true transition state(s) time=   6.54
 isnewts> transition state is the same as number        3 energy=     -384.9345330389
 tryconnect> Will not repeat search for TS      2 same as TS      3

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     846 steps. Energy=    -389.1046918       time=       2.12
 Minus side of path:                    1001 steps. Energy=    -390.5554047       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1046918 0.40270E-01     -389.0644215  1.4910         -390.5554047  13.830  12.858  10.501  13.808
        Known (#2)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 5_F and 9_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0626 Dev= 0.13% S= 15.64 time= 0.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   7.36

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     925 steps. Energy=    -388.6809028       time=       3.00
 Minus side of path:                     895 steps. Energy=    -388.5796269       time=       2.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6809028 0.14356         -388.5373394 0.42288E-01     -388.5796269  15.726  15.593   2.038  71.141
        Known (#5)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -389.2335056  2.9859        -386.2475829  2.2043        -388.4519192  32.790  29.513   4.087  35.482
   4     -388.4519192 0.91649        -387.5354327 0.70317        -388.2386015  21.724  18.872   3.275  44.274
   7     -388.2386015 0.87707        -387.3615291  1.2181        -388.5796269  14.127  13.006   2.084  69.582
   9     -388.5796269 0.42288E-01    -388.5373394 0.14356        -388.6809028  15.726  15.593   2.038  71.141
   2     -388.6809028  3.7826        -384.8983285 0.50217        -385.4005012  20.588  19.381   2.513  57.696
   6     -385.4005012 0.24639E-01    -385.3758621 0.36197E-01    -385.4120596   1.536   1.526   2.960  48.991
   3     -385.4120596 0.47753        -384.9345330  5.6209        -390.5554047  13.458  11.904   7.852  18.467
   8     -390.5554047  1.4910        -389.0644215 0.40270E-01    -389.1046918  13.830  12.858  10.501  13.808

 Number of TS in the path       =      8
 Number of cycles               =      4

 Elapsed time=                               132.22
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             50594 time=          67.41 %= 51.0
 OPTIM> # of energy+gradient+Hessian calls=       413 time=           1.97 %=  1.5
