
 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)@comp28.ch.
                 Created on  5/28/12 at 12:44: 8 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=    -391.4617264     RMS force=    0.9202775967E-06
 OPTIM> Final energy  =    -391.2684032     RMS force=    0.9870640645E-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=     27228.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.08     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1449 Dev= 2.59% S= 36.17 time= 4.33
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        114
 DNEB run yielded 1 true transition state(s) time=  11.07

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1002 steps. Energy=    -389.8533544       time=       4.70
 Minus side of path:                     951 steps. Energy=    -389.9345728       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.8533544  1.2944         -388.5589412  1.3756         -389.9345728  23.375  22.117   2.683  54.036
        *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      3 steps with      2 missing connections, weight=     4846.5    
 decide> The unconnected minima in the chain and their distances are:
     2        9.29     4     3       15.93     1 
 

 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= 0.3416 Dev= 0.13% S= 9.46 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   6.77

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     902 steps. Energy=    -389.9345728       time=       2.85
 Minus side of path:                     957 steps. Energy=    -391.2684032       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.9345728 0.92399         -389.0105865  2.2578         -391.2684032  12.233   9.294   6.660  21.771
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2924 Dev= 0.78% S= 16.81 time= 0.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.42

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1080 steps. Energy=    -391.4356342       time=       3.27
 Minus side of path:                     853 steps. Energy=    -389.8533544       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4356342  1.6115         -389.8241123 0.29242E-01     -389.8533544  17.616  17.181   3.120  46.475
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     8088.9    
 decide> The unconnected minima in the chain and their distances are:
     3       15.93     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 805 RMS= 0.0382 Dev= 4.01% S= 23.14 time= 27.71
 Following    4 images are candidates for TS:    6   15   21   23  
 Converged to TS (number of iterations):         37
 Converged to TS (number of iterations):         60
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):         29
 DNEB run yielded 4 true transition state(s) time=  27.73

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     879 steps. Energy=    -391.4617264       time=       2.11
 Minus side of path:                     940 steps. Energy=    -393.6609809       time=       2.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4617264 0.20702         -391.2547094  2.4063         -393.6609809  12.145  11.189   4.884  29.689
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     948 steps. Energy=    -393.1264313       time=       3.12
 Minus side of path:                    1047 steps. Energy=    -393.6609809       time=       3.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.1264313 0.59545         -392.5309817  1.1300         -393.6609809  19.613  13.659   9.120  15.899
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to S set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     913 steps. Energy=    -391.1689352       time=       2.95
 Minus side of path:                     913 steps. Energy=    -393.6609809       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1689352 0.64227         -390.5266678  3.1343         -393.6609809   5.857   5.369   7.344  19.745
        *NEW* (Placed in 8)                                     Known (#6)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     854 steps. Energy=    -391.4243538       time=       2.26
 Minus side of path:                     831 steps. Energy=    -392.0698724       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4243538 0.65502         -390.7693294  1.3005         -392.0698724   3.184   3.067  22.461   6.456
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     137.11    
 decide> The unconnected minima in the chain and their distances are:
     3        5.16     7 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1597 Dev= 0.26% S= 5.33 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   8.24
 isnewts> transition state is the same as number        7 energy=     -390.7693293708
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     868 steps. Energy=    -391.4243538       time=       2.10
 Minus side of path:                     843 steps. Energy=    -392.0698724       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4243538 0.65502         -390.7693294  1.3005         -392.0698724   3.184   3.067  22.460   6.456
        Known (#9)                                              Known (#10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     274.22    
 decide> The unconnected minima in the chain and their distances are:
     3        5.16     7 
 

 tryconnect> 385-iteration DNEB run for minima 3_F and 7_S using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 385 RMS= 0.0253 Dev= 2.39% S= 7.62 time= 6.37
 Following    2 images are candidates for TS:    1    6  
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):         22
 DNEB run yielded 2 true transition state(s) time=   9.85
 isnewts> transition state is the same as number        7 energy=     -390.7693293699
 tryconnect> Will not repeat search for TS      1 same as TS      7
 isnewts> transition state is the same as number        6 energy=     -390.5266677759
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     914 steps. Energy=    -391.1689352       time=       2.25
 Minus side of path:                     873 steps. Energy=    -393.6609809       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1689352 0.64227         -390.5266678  3.1343         -393.6609809   5.857   5.369   7.336  19.764
        Known (#8)                                              Known (#6)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     411.33    
 decide> The unconnected minima in the chain and their distances are:
     3        5.16     7 
 

 tryconnect> 770-iteration DNEB run for minima 3_F and 7_S using 22 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 770 RMS= 0.0268 Dev= 2.31% S= 7.97 time= 24.60
 Following    2 images are candidates for TS:    2   11  
 Converged to TS (number of iterations):         24
 Converged to TS (number of iterations):         22
 DNEB run yielded 2 true transition state(s) time=   9.61
 isnewts> transition state is the same as number        7 energy=     -390.7693293708
 tryconnect> Will not repeat search for TS      1 same as TS      7
 isnewts> transition state is the same as number        6 energy=     -390.5266677759
 tryconnect> Will not repeat search for TS      2 same as TS      6
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     959.10    
 decide> The unconnected minima in the chain and their distances are:
     3        9.86     8 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2114 Dev= 0.23% S= 10.12 time= 0.26
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   6.18

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     863 steps. Energy=    -391.4356342       time=       2.50
 Minus side of path:                     870 steps. Energy=    -392.0698724       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4356342 0.69070         -390.7449373  1.3249         -392.0698724   3.649   3.439  16.448   8.816
        Known (#5)                                              Known (#10)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1918.2    
 decide> The unconnected minima in the chain and their distances are:
     3        9.86     8 
 

 tryconnect> 770-iteration DNEB run for minima 3_F and 8_S using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 770 RMS= 0.0293 Dev= 6.60% S= 13.06 time= 24.87
 Following    4 images are candidates for TS:    2    6    8   15  
 Converged to TS (number of iterations):         26
 Converged to TS (number of iterations):        120
 Converged to TS (number of iterations):        112
 Converged to TS (number of iterations):         29
 DNEB run yielded 4 true transition state(s) time=  29.72
 isnewts> transition state is the same as number        7 energy=     -390.7693293708
 tryconnect> Will not repeat search for TS      1 same as TS      7
 isnewts> transition state is the same as number       11 energy=     -389.5311083806
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1088 steps. Energy=    -391.2244416       time=       3.03
 Minus side of path:                     905 steps. Energy=    -389.5910800       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2244416  1.6933         -389.5311084 0.59972E-01     -389.5910800  17.631  15.244   4.359  33.265
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.

 >>>>>  Path run for ts 12 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     888 steps. Energy=    -389.5910800       time=       2.08
 Minus side of path:                    1094 steps. Energy=    -391.2244416       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.5910800 0.59972E-01     -389.5311084  1.6933         -391.2244416  17.631  15.244   4.362  33.240
        Known (#12)                                             Known (#11)
 Connection established between members of the U set.

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     834 steps. Energy=    -391.1689352       time=       1.91
 Minus side of path:                     895 steps. Energy=    -391.2244416       time=       2.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1689352 0.68234E-01     -391.1007010 0.12374         -391.2244416   7.511   7.098   2.463  58.878
        Known (#8)                                              Known (#11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 12 minima and 13 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     775.42    
 decide> The unconnected minima in the chain and their distances are:
    10        9.19    11 
 

 tryconnect> 70-iteration DNEB run for minima 10_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0650 Dev= 0.01% S= 9.19 time= 0.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.58

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     924 steps. Energy=    -391.2244416       time=       3.47
 Minus side of path:                     875 steps. Energy=    -392.0698724       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2244416 0.11860         -391.1058370 0.96404         -392.0698724   9.552   9.188   2.406  60.268
        Known (#11)                                             Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -391.4617264 0.20702        -391.2547094  2.4063        -393.6609809  12.145  11.189   4.884  29.689
   6     -393.6609809  3.1343        -390.5266678 0.64227        -391.1689352   5.857   5.369   7.344  19.745
  13     -391.1689352 0.68234E-01    -391.1007010 0.12374        -391.2244416   7.511   7.098   2.463  58.878
  14     -391.2244416 0.11860        -391.1058370 0.96404        -392.0698724   9.552   9.188   2.406  60.268
  10     -392.0698724  1.3249        -390.7449373 0.69070        -391.4356342   3.649   3.439  16.448   8.816
   3     -391.4356342  1.6115        -389.8241123 0.29242E-01    -389.8533544  17.616  17.181   3.120  46.475
   1     -389.8533544  1.2944        -388.5589412  1.3756        -389.9345728  23.375  22.117   2.683  54.036
   2     -389.9345728 0.92399        -389.0105865  2.2578        -391.2684032  12.233   9.294   6.660  21.771

 Number of TS in the path       =      8
 Number of cycles               =      9

 Elapsed time=                               285.17
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            107050 time=         153.76 %= 53.9
 OPTIM> # of energy+gradient+Hessian calls=       879 time=           4.54 %=  1.6
