
 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)@comp24.ch.
                 Created on  5/28/12 at 12:38:12 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -376.8434946     RMS force=    0.9352800497E-06
 OPTIM> Final energy  =    -385.2394514     RMS force=    0.9243098185E-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=    0.21942E+06
 decide> The unconnected minima in the chain and their distances are:
     2       60.31     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 2_F using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 630 RMS= 0.0494 Dev= 4.85% S= 74.76 time= 13.35
 Following    3 images are candidates for TS:    4    8   14  
 Converged to TS (number of iterations):         58
 Converged to TS (number of iterations):        192
 Converged to TS (number of iterations):         75
 DNEB run yielded 3 true transition state(s) time=  30.25
 isnewts> transition state is the same as number        2 energy=     -381.9539938395
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1048 steps. Energy=    -376.8434946       time=       3.33
 Minus side of path:                    2294 steps. Energy=    -386.6404421       time=      18.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.8434946 0.81899E-01     -376.7615954  9.8788         -386.6404421  70.810  67.547   1.976  73.390
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     959 steps. Energy=    -381.9741642       time=       3.43
 Minus side of path:                    1078 steps. Energy=    -382.9986292       time=       4.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.9741642 0.20170E-01     -381.9539938  1.0446         -382.9986292  19.500  18.655   3.134  46.273
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1037 steps. Energy=    -382.9986292       time=       2.48
 Minus side of path:                     980 steps. Energy=    -381.9741642       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9986292  1.0446         -381.9539938 0.20170E-01     -381.9741642  19.500  18.654   3.132  46.296
        Known (#5)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     41399.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.59     3 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 3_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0478 Dev= 2.44% S= 40.16 time= 4.55
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=   7.17

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     928 steps. Energy=    -383.1759484       time=       2.04
 Minus side of path:                    1043 steps. Energy=    -386.0833114       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.1759484 0.18827E-02     -383.1740658  2.9092         -386.0833114  11.204  10.500   5.610  25.849
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     31318.    
 decide> The unconnected minima in the chain and their distances are:
     2        8.70     7     6       31.30     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1066 Dev= 0.01% S= 8.73 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.71

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     987 steps. Energy=    -385.8967771       time=       2.27
 Minus side of path:                     999 steps. Energy=    -385.2394514       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8967771 0.67456         -385.2222203 0.17231E-01     -385.2394514   6.955   5.982   6.934  20.913
        *NEW* (Placed in 8)                                     Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 3_S and 6_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0559 Dev= 0.76% S= 33.69 time= 3.69
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   5.66

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     966 steps. Energy=    -383.1163545       time=       2.17
 Minus side of path:                     974 steps. Energy=    -383.1759484       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.1163545 0.23386E-01     -383.0929686 0.82980E-01     -383.1759484   3.992   3.967   2.560  56.634
        *NEW* (Placed in 9)                                     Known (#6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     29743.    
 decide> The unconnected minima in the chain and their distances are:
     8        6.28     7     9       30.90     3 
 

 tryconnect> 70-iteration DNEB run for minima 7_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0356 Dev= 0.02% S= 6.29 time= 0.24
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   4.50

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     912 steps. Energy=    -385.8967771       time=       1.99
 Minus side of path:                    1007 steps. Energy=    -386.0833114       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8967771 0.65498E-03     -385.8961222 0.18719         -386.0833114   6.295   6.279   2.166  66.948
        Known (#8)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 3_S and 9_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1659 Dev= 0.42% S= 33.27 time= 3.67
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.26

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1028 steps. Energy=    -384.3053721       time=       2.43
 Minus side of path:                    1035 steps. Energy=    -383.1759484       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3053721  2.6030         -381.7023782  1.4736         -383.1759484  28.182  23.040   2.523  57.464
        *NEW* (Placed in 10)                                    Known (#6)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     3571.5    
 decide> The unconnected minima in the chain and their distances are:
    10       15.29     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1378 Dev= 0.08% S= 15.64 time= 0.78
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         84
 DNEB run yielded 1 true transition state(s) time=   6.13

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1112 steps. Energy=    -386.1124329       time=       2.78
 Minus side of path:                    1003 steps. Energy=    -384.5091216       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1124329  1.6115         -384.5009631 0.81585E-02     -384.5091216  15.441  15.257   2.412  60.110
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     888.39    
 decide> The unconnected minima in the chain and their distances are:
    10        4.27    12    11        9.32     3 
 

 tryconnect> 70-iteration DNEB run for minima 10_F and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0744 Dev= 0.01% S= 4.28 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   3.99

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     953 steps. Energy=    -384.3053721       time=       2.14
 Minus side of path:                     962 steps. Energy=    -384.4970863       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3053721 0.49321E-02     -384.3004400 0.19665         -384.4970863   3.151   3.146   3.650  39.728
        Known (#10)                                             *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1511 Dev= 0.18% S= 9.40 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   4.44

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1009 steps. Energy=    -386.6404421       time=       2.35
 Minus side of path:                     999 steps. Energy=    -386.1715440       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.6404421 0.48139         -386.1590535 0.12490E-01     -386.1715440   6.481   6.282   3.966  36.562
        Known (#3)                                              *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 14 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      2 missing connections, weight=     110.73    
 decide> The unconnected minima in the chain and their distances are:
    13        2.05    12    11        4.67    14 
 

 tryconnect> 70-iteration DNEB run for minima 12_U and 13_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0097 Dev= 0.03% S= 2.05 time= 0.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.09

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     992 steps. Energy=    -384.5091216       time=       2.31
 Minus side of path:                     983 steps. Energy=    -384.4970863       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.5091216 0.41915E-01     -384.4672063 0.29880E-01     -384.4970863   2.069   2.051   2.469  58.728
        Known (#12)                                             Known (#13)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 11_F and 14_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0294 Dev= 0.07% S= 4.69 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.49

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                    1022 steps. Energy=    -386.1124329       time=       2.38
 Minus side of path:                    1000 steps. Energy=    -386.1715440       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1124329 0.93397E-02     -386.1030932 0.68451E-01     -386.1715440   5.463   4.674   6.771  21.415
        Known (#11)                                             Known (#14)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -376.8434946 0.81899E-01    -376.7615954  9.8788        -386.6404421  70.810  67.547   1.976  73.390
  11     -386.6404421 0.48139        -386.1590535 0.12490E-01    -386.1715440   6.481   6.282   3.966  36.562
  13     -386.1715440 0.68451E-01    -386.1030932 0.93397E-02    -386.1124329   5.463   4.674   6.771  21.415
   9     -386.1124329  1.6115        -384.5009631 0.81585E-02    -384.5091216  15.441  15.257   2.412  60.110
  12     -384.5091216 0.41915E-01    -384.4672063 0.29880E-01    -384.4970863   2.069   2.051   2.469  58.728
  10     -384.4970863 0.19665        -384.3004400 0.49321E-02    -384.3053721   3.151   3.146   3.650  39.728
   8     -384.3053721  2.6030        -381.7023782  1.4736        -383.1759484  28.182  23.040   2.523  57.464
   4     -383.1759484 0.18827E-02    -383.1740658  2.9092        -386.0833114  11.204  10.500   5.610  25.849
   7     -386.0833114 0.18719        -385.8961222 0.65498E-03    -385.8967771   6.295   6.279   2.166  66.948
   5     -385.8967771 0.67456        -385.2222203 0.17231E-01    -385.2394514   6.955   5.982   6.934  20.913

 Number of TS in the path       =     10
 Number of cycles               =      7

 Elapsed time=                               184.58
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             62972 time=          76.84 %= 41.6
 OPTIM> # of energy+gradient+Hessian calls=       814 time=           3.32 %=  1.8
