
 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)@comp29.ch.
                 Created on  5/28/12 at 12:45:15 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -381.3469114     RMS force=    0.9354232431E-06
 OPTIM> Final energy  =    -385.2780020     RMS force=    0.9419005855E-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=    0.31828E+06
 decide> The unconnected minima in the chain and their distances are:
     2       68.28     1 
 

 tryconnect> 700-iteration DNEB run for minima 1_S and 2_F using 20 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9243305120E-01
 Double-ended search iterations= 700 RMS= 0.0938 Dev= 6.54% S= 86.28 time= 16.94
 Following    2 images are candidates for TS:    9   20  
 Converged to TS (number of iterations):        145
 Converged to TS (number of iterations):         21
 DNEB run yielded 2 true transition state(s) time=  19.46

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1009 steps. Energy=    -382.3109912       time=       3.11
 Minus side of path:                    1242 steps. Energy=    -381.3066617       time=       4.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.3109912  3.5522         -378.7587619  2.5479         -381.3066617  48.752  46.180   2.107  68.828
        *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:                    1433 steps. Energy=    -389.5240203       time=       5.36
 Minus side of path:                     945 steps. Energy=    -385.2780020       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.5240203  4.4022         -385.1218190 0.15618         -385.2780020  33.712  31.907   1.812  80.018
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=    0.12031E+06
 decide> The unconnected minima in the chain and their distances are:
     2       49.35     3     4        4.94     1 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 3_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.1299 Dev= 3.33% S= 61.83 time= 8.46
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   8.19

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     953 steps. Energy=    -380.4822494       time=       2.19
 Minus side of path:                    1023 steps. Energy=    -380.6469630       time=       2.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.4822494 0.14393E-02     -380.4808101 0.16615         -380.6469630   1.125   1.119   5.728  25.314
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 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= 0.0105 Dev= 0.01% S= 4.95 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.48

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     963 steps. Energy=    -381.3066617       time=       2.54
 Minus side of path:                    1001 steps. Energy=    -381.3469114       time=       2.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3066617 0.10733E-03     -381.3065543 0.40357E-01     -381.3469114   4.961   4.945   2.063  70.289
        Known (#4)                                              Known (#1)
 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=    0.12648E+06
 decide> The unconnected minima in the chain and their distances are:
     5       50.20     3 
 

 tryconnect> 525-iteration DNEB run for minima 3_S and 5_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 525 RMS= 0.0948 Dev= 7.22% S= 63.39 time= 9.91
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        122
 DNEB run yielded 1 true transition state(s) time=   9.27

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1244 steps. Energy=    -387.7092471       time=       4.73
 Minus side of path:                    2014 steps. Energy=    -386.7175464       time=      16.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.7092471  10.389         -377.3199623  9.3976         -386.7175464  71.371  64.245   1.735  83.556
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=    0.12243E+06
 decide> The unconnected minima in the chain and their distances are:
     5       40.15     8     9       38.65     3 
 

 tryconnect> 420-iteration DNEB run for minima 5_F and 8_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 420 RMS= 0.1075 Dev= 3.07% S= 50.13 time= 6.91
 Following    2 images are candidates for TS:    5   10  
 Converged to TS (number of iterations):         71
 Converged to TS (number of iterations):         57
 DNEB run yielded 2 true transition state(s) time=  12.42

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1235 steps. Energy=    -393.5152156       time=       4.19
 Minus side of path:                    1058 steps. Energy=    -389.5240203       time=       3.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.5152156  7.1023         -386.4128795  3.1111         -389.5240203  43.380  38.276   2.281  63.582
        *NEW* (Placed in 10)                                    Known (#5)
 Unconnected minimum 10 found its way to F set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1005 steps. Energy=    -387.6615209       time=       3.35
 Minus side of path:                    1004 steps. Energy=    -393.5152156       time=       2.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.6615209  3.8530         -383.8085340  9.7067         -393.5152156  19.556  14.047   5.257  27.582
        *NEW* (Placed in 11)                                    Known (#10)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 3_S and 9_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0715 Dev= 2.46% S= 42.59 time= 5.15
 Following    2 images are candidates for TS:    5    8  
 Converged to TS (number of iterations):        115
 Converged to TS (number of iterations):        141
 DNEB run yielded 2 true transition state(s) time=  21.93

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1000 steps. Energy=    -382.5385513       time=       3.04
 Minus side of path:                     980 steps. Energy=    -382.5608937       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5385513 0.12004         -382.4185136 0.14238         -382.5608937   9.639   8.242   3.593  40.353
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1069 steps. Energy=    -382.7784182       time=       2.90
 Minus side of path:                    1352 steps. Energy=    -384.8081496       time=       5.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.7784182 0.19734         -382.5810809  2.2271         -384.8081496  45.557  42.496   1.779  81.518
        *NEW* (Placed in 14)                                    *NEW* (Placed in 15)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 15 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      4 missing connections, weight=     28314.    
 decide> The unconnected minima in the chain and their distances are:
    11        1.08     8     9       17.99    14    14        1.70    13    12       28.23     3 
 

 tryconnect> 70-iteration DNEB run for minima 8_U and 11_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0177 Dev= 0.10% S= 1.09 time= 0.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   3.13

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     935 steps. Energy=    -387.7092471       time=       3.03
 Minus side of path:                     960 steps. Energy=    -387.6615209       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.7092471 0.55992E-01     -387.6532548 0.82661E-02     -387.6615209   1.088   1.083   5.298  27.366
        Known (#8)                                              Known (#11)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 9_F and 14_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.3323 Dev= 0.67% S= 18.48 time= 1.14
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   4.94

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1087 steps. Energy=    -382.7784182       time=       3.25
 Minus side of path:                    1050 steps. Energy=    -386.7175464       time=       3.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.7784182 0.14148         -382.6369370  4.0806         -386.7175464  22.239  18.003   2.065  70.212
        Known (#14)                                             Known (#9)
 Unconnected minimum 14 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 13_U and 14_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1650 Dev= 0.37% S= 1.87 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.55

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     978 steps. Energy=    -382.7784182       time=       2.47
 Minus side of path:                     978 steps. Energy=    -382.5608937       time=       2.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.7784182 0.89133         -381.8870845 0.67381         -382.5608937   1.835   1.698 130.114   1.114
        Known (#14)                                             Known (#13)
 Unconnected minimum 13 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 3_S and 12_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0243 Dev= 0.04% S= 28.75 time= 2.72
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.42

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     972 steps. Energy=    -382.5385513       time=       2.79
 Minus side of path:                     969 steps. Energy=    -382.3109912       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5385513 0.46169         -382.0768607 0.23413         -382.3109912  29.000  28.239   3.080  47.073
        Known (#12)                                             Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -381.3469114 0.40357E-01    -381.3065543 0.10733E-03    -381.3066617   4.961   4.945   2.063  70.289
   1     -381.3066617  2.5479        -378.7587619  3.5522        -382.3109912  48.752  46.180   2.107  68.828
  13     -382.3109912 0.23413        -382.0768607 0.46169        -382.5385513  29.000  28.239   3.080  47.073
   8     -382.5385513 0.12004        -382.4185136 0.14238        -382.5608937   9.639   8.242   3.593  40.353
  12     -382.5608937 0.67381        -381.8870845 0.89133        -382.7784182   1.835   1.698 130.114   1.114
  11     -382.7784182 0.14148        -382.6369370  4.0806        -386.7175464  22.239  18.003   2.065  70.212
   5     -386.7175464  9.3976        -377.3199623  10.389        -387.7092471  71.371  64.245   1.735  83.556
  10     -387.7092471 0.55992E-01    -387.6532548 0.82661E-02    -387.6615209   1.088   1.083   5.298  27.366
   7     -387.6615209  3.8530        -383.8085340  9.7067        -393.5152156  19.556  14.047   5.257  27.582
   6     -393.5152156  7.1023        -386.4128795  3.1111        -389.5240203  43.380  38.276   2.281  63.582
   2     -389.5240203  4.4022        -385.1218190 0.15618        -385.2780020  33.712  31.907   1.812  80.018

 Number of TS in the path       =     11
 Number of cycles               =      5

 Elapsed time=                               239.54
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             84405 time=         102.05 %= 42.6
 OPTIM> # of energy+gradient+Hessian calls=       856 time=           3.83 %=  1.6
