
 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)@comp26.ch.
                 Created on  5/28/12 at 13: 7:12 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -386.1053788     RMS force=    0.9501329568E-06
 OPTIM> Final energy  =    -396.8219334     RMS force=    0.7851346602E-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=     52419.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.43     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 385 RMS= 0.1397 Dev= 4.23% S= 42.29 time= 6.11
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        149
 DNEB run yielded 1 true transition state(s) time=  14.03

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1355 steps. Energy=    -390.3044736       time=       7.21
 Minus side of path:                     985 steps. Energy=    -387.2365477       time=       4.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3044736  6.2050         -384.0994455  3.1371         -387.2365477  27.166  20.207   7.972  18.189
        *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=     48706.    
 decide> The unconnected minima in the chain and their distances are:
     2       10.43     4     4       36.23     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 0.4209 Dev= 0.58% S= 11.45 time= 0.49
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   4.83

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     903 steps. Energy=    -388.5631391       time=       2.22
 Minus side of path:                     959 steps. Energy=    -396.8219334       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5631391 0.19154         -388.3715992  8.4503         -396.8219334  12.238  10.053   5.445  26.630
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 4_U using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7909635100    
 Double-ended search iterations= 350 RMS= 0.0812 Dev= 0.58% S= 39.48 time= 4.85
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        132
 DNEB run yielded 1 true transition state(s) time=  10.50

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     957 steps. Energy=    -389.9957168       time=       2.42
 Minus side of path:                    1003 steps. Energy=    -390.3044736       time=       2.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.9957168 0.82905         -389.1666716  1.1378         -390.3044736  16.353  14.187   3.284  44.158
        *NEW* (Placed in 6)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     53495.    
 decide> The unconnected minima in the chain and their distances are:
     5       37.68     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 5_F using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.1461 Dev= 3.34% S= 44.83 time= 5.94
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        172
 DNEB run yielded 1 true transition state(s) time=  14.21

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     933 steps. Energy=    -389.2382802       time=       3.22
 Minus side of path:                    1067 steps. Energy=    -388.4421440       time=       3.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2382802  2.7909         -386.4473900  1.9948         -388.4421440  17.815  16.845   4.318  33.582
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     62088.    
 decide> The unconnected minima in the chain and their distances are:
     5        6.69     4     3       39.53     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7623 Dev= 0.30% S= 6.83 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   5.13

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     927 steps. Energy=    -387.2365477       time=       3.64
 Minus side of path:                     934 steps. Energy=    -388.5691851       time=       3.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.2365477 0.34501         -386.8915351  1.6777         -388.5691851   7.863   6.926   5.076  28.564
        Known (#4)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 3_U using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 385 RMS= 0.0924 Dev= 1.18% S= 42.32 time= 5.89
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        107
 DNEB run yielded 1 true transition state(s) time=   7.84

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     973 steps. Energy=    -385.9147220       time=       2.50
 Minus side of path:                    1006 steps. Energy=    -386.1053788       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9147220 0.19669         -385.7180324 0.38735         -386.1053788  17.689  16.887   3.996  36.283
        *NEW* (Placed in 10)                                    Known (#1)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     18372.    
 decide> The unconnected minima in the chain and their distances are:
     5        1.08     9     4       26.39    10 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 9_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0309 Dev= 0.04% S= 1.08 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.65

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     856 steps. Energy=    -388.5691851       time=       2.06
 Minus side of path:                     865 steps. Energy=    -388.5631391       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5691851 0.56192E-01     -388.5129926 0.50147E-01     -388.5631391   1.089   1.080   6.007  24.140
        Known (#9)                                              Known (#5)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 4_F and 10_S using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0592 Dev= 0.77% S= 27.50 time= 2.33
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.38
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     20059.    
 decide> The unconnected minima in the chain and their distances are:
     6       27.17    10 
 

 tryconnect> 280-iteration DNEB run for minima 6_F and 10_S using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.3828 Dev= 0.16% S= 28.38 time= 3.07
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.09

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     915 steps. Energy=    -385.9147220       time=       2.12
 Minus side of path:                    1207 steps. Energy=    -390.3044736       time=       3.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9147220 0.20461E-02     -385.9126758  4.3918         -390.3044736  29.907  29.578   1.925  75.316
        Known (#10)                                             Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -386.1053788 0.38735        -385.7180324 0.19669        -385.9147220  17.689  16.887   3.996  36.283
   8     -385.9147220 0.20461E-02    -385.9126758  4.3918        -390.3044736  29.907  29.578   1.925  75.316
   1     -390.3044736  6.2050        -384.0994455  3.1371        -387.2365477  27.166  20.207   7.972  18.189
   5     -387.2365477 0.34501        -386.8915351  1.6777        -388.5691851   7.863   6.926   5.076  28.564
   7     -388.5691851 0.56192E-01    -388.5129926 0.50147E-01    -388.5631391   1.089   1.080   6.007  24.140
   2     -388.5631391 0.19154        -388.3715992  8.4503        -396.8219334  12.238  10.053   5.445  26.630

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

 Elapsed time=                               166.03
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             47135 time=          63.97 %= 38.5
 OPTIM> # of energy+gradient+Hessian calls=       954 time=           4.89 %=  2.9
