
 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)@comp25.ch.
                 Created on  5/28/12 at 12:51:52 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -381.7654884     RMS force=    0.8830557765E-06
 OPTIM> Final energy  =    -378.7713696     RMS force=    0.8923153024E-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=    0.10210E+06
 decide> The unconnected minima in the chain and their distances are:
     2       46.74     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.1520 Dev= 2.84% S= 56.47 time= 9.61
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        143
 DNEB run yielded 1 true transition state(s) time=  11.25

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     956 steps. Energy=    -378.5378511       time=       2.54
 Minus side of path:                    1049 steps. Energy=    -384.1515345       time=       3.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.5378511 0.79041E-01     -378.4588096  5.6927         -384.1515345  20.666  19.333   6.790  21.355
        *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      2 steps with      2 missing connections, weight=     46903.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.81     3     3       28.43     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0678 Dev= 0.75% S= 31.09 time= 3.04
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.54

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0767 Dev= 0.32% S= 29.94 time= 3.09
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    8  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=   8.01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1110 steps. Energy=    -381.7654884       time=       4.07
 Minus side of path:                    1067 steps. Energy=    -386.4567933       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7654884  2.9552         -378.8102945  7.6465         -386.4567933  45.122  36.686   3.564  40.682
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     44500.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.31     4     4       19.60     5 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 4_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5098621309    
 Double-ended search iterations= 315 RMS= 0.0647 Dev= 0.49% S= 37.08 time= 3.99
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   7.05

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1112 steps. Energy=    -384.1515345       time=       3.65
 Minus side of path:                     959 steps. Energy=    -378.5010307       time=       2.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1515345  7.9211         -376.2303998  2.2706         -378.5010307  38.648  35.401   2.777  52.217
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 4_U and 5_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1430 Dev= 0.18% S= 20.25 time= 1.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   5.17

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     935 steps. Energy=    -384.1515345       time=       3.16
 Minus side of path:                     985 steps. Energy=    -385.4120429       time=       3.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1515345 0.95769E-01     -384.0557650  1.3563         -385.4120429  10.833   9.622   2.726  53.193
        Known (#4)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     9419.9    
 decide> The unconnected minima in the chain and their distances are:
     2       16.55     6     7       16.97     5 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0479 Dev= 0.13% S= 16.67 time= 0.85
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.98

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     995 steps. Energy=    -379.0114533       time=       2.59
 Minus side of path:                     893 steps. Energy=    -378.5010307       time=       2.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.0114533  1.0556         -377.9558608 0.54517         -378.5010307  10.138   8.408   2.174  66.704
        *NEW* (Placed in 8)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 5_S and 7_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0675 Dev= 0.15% S= 17.68 time= 1.26
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.48

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     902 steps. Energy=    -385.4120429       time=       2.13
 Minus side of path:                     963 steps. Energy=    -386.4567933       time=       2.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4120429 0.43677E-01     -385.3683654  1.0884         -386.4567933  17.788  17.001  12.737  11.384
        Known (#7)                                              Known (#5)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     2168.6    
 decide> The unconnected minima in the chain and their distances are:
     2       12.94     8 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0733 Dev= 0.05% S= 12.98 time= 0.50
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   4.13

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     908 steps. Energy=    -378.7713696       time=       2.24
 Minus side of path:                     945 steps. Energy=    -378.8074464       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.7713696 0.11229         -378.6590787 0.14837         -378.8074464   5.414   5.317   3.288  44.106
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1155.4    
 decide> The unconnected minima in the chain and their distances are:
     9       10.49     8 
 

 tryconnect> 105-iteration DNEB run for minima 8_S and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0421 Dev= 0.03% S= 10.53 time= 0.50
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.76

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     919 steps. Energy=    -378.8074464       time=       2.99
 Minus side of path:                     933 steps. Energy=    -379.0114533       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.8074464 0.28066E-01     -378.7793805 0.23207         -379.0114533  10.541  10.493  12.002  12.081
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -381.7654884  2.9552        -378.8102945  7.6465        -386.4567933  45.122  36.686   3.564  40.682
   6     -386.4567933  1.0884        -385.3683654 0.43677E-01    -385.4120429  17.788  17.001  12.737  11.384
   4     -385.4120429  1.3563        -384.0557650 0.95769E-01    -384.1515345  10.833   9.622   2.726  53.193
   3     -384.1515345  7.9211        -376.2303998  2.2706        -378.5010307  38.648  35.401   2.777  52.217
   5     -378.5010307 0.54517        -377.9558608  1.0556        -379.0114533  10.138   8.408   2.174  66.704
   8     -379.0114533 0.23207        -378.7793805 0.28066E-01    -378.8074464  10.541  10.493  12.002  12.081
   7     -378.8074464 0.14837        -378.6590787 0.11229        -378.7713696   5.414   5.317   3.288  44.106

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

 Elapsed time=                               141.19
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             42592 time=          56.67 %= 40.1
 OPTIM> # of energy+gradient+Hessian calls=       679 time=           3.40 %=  2.4
