
 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)@comp18.ch.
                 Created on  5/28/12 at 13: 6:45 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=    -389.7163378     RMS force=    0.9842381170E-06
 OPTIM> Final energy  =    -386.2896343     RMS force=    0.8147186892E-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=     82663.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.56     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      17.10339358    
 Double-ended search iterations= 455 RMS= 0.4255 Dev= 0.52% S= 46.70 time= 7.91
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   5.81

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1147 steps. Energy=    -392.8573233       time=       3.01
 Minus side of path:                     984 steps. Energy=    -385.8281028       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8573233  7.3210         -385.5363475 0.29176         -385.8281028  26.397  24.279   2.371  61.166
        *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=     31471.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.94     4     3       25.18     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 245 RMS= 0.1119 Dev= 0.21% S= 25.94 time= 2.32
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   5.57

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     979 steps. Energy=    -386.2896343       time=       2.30
 Minus side of path:                     950 steps. Energy=    -385.2565250       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2896343  1.4451         -384.8445499 0.41198         -385.2565250   6.553   5.627   8.005  18.114
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_U using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      22.92018318    
 Double-ended search iterations= 245 RMS= 0.4202 Dev= 0.36% S= 25.70 time= 2.25
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   6.57

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     948 steps. Energy=    -389.7212947       time=       2.08
 Minus side of path:                     976 steps. Energy=    -389.7163378       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7212947 0.16040E-01     -389.7052551 0.11083E-01     -389.7163378   0.991   0.983   3.152  46.006
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     27299.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.56     4     3       25.10     6 
 

 tryconnect> 210-iteration DNEB run for minima 4_U and 5_F using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0850 Dev= 0.31% S= 23.51 time= 1.70
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.42

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     983 steps. Energy=    -385.1135753       time=       2.31
 Minus side of path:                    1027 steps. Energy=    -385.8281028       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1135753  1.0124         -384.1011549  1.7269         -385.8281028  23.366  20.221   4.995  29.026
        *NEW* (Placed in 7)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 3_U and 6_S using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      22.92018318    
 Double-ended search iterations= 245 RMS= 0.2741 Dev= 0.09% S= 25.61 time= 2.25
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   4.96

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     960 steps. Energy=    -390.7922733       time=       2.17
 Minus side of path:                     986 steps. Energy=    -389.7163378       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7922733  2.7305         -388.0618092  1.6545         -389.7163378  21.534  19.914   2.842  51.028
        *NEW* (Placed in 8)                                     Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     6921.5    
 decide> The unconnected minima in the chain and their distances are:
     5        8.21     7     3       18.54     8 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0336 Dev= 0.00% S= 8.21 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.94

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     946 steps. Energy=    -385.2565250       time=       2.16
 Minus side of path:                     942 steps. Energy=    -385.1135753       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2565250 0.25254         -385.0039875 0.10959         -385.1135753   8.289   8.207   3.597  40.311
        Known (#5)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_F and 8_S using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 175 RMS= 0.4218 Dev= 0.26% S= 19.03 time= 1.19
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.08

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     968 steps. Energy=    -390.1392465       time=       2.23
 Minus side of path:                     958 steps. Energy=    -390.7922733       time=       2.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1392465 0.32480E-01     -390.1067664 0.68551         -390.7922733  10.688  10.427   3.424  42.350
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     9423.8    
 decide> The unconnected minima in the chain and their distances are:
     3       21.12     9 
 

 tryconnect> 210-iteration DNEB run for minima 3_F and 9_S using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 210 RMS= 0.0565 Dev= 0.19% S= 21.69 time= 1.71
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   3.81

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     981 steps. Energy=    -392.8573233       time=       2.27
 Minus side of path:                     942 steps. Energy=    -390.1392465       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8573233  2.7839         -390.0733882 0.65858E-01     -390.1392465  21.807  21.131   7.872  18.420
        Known (#3)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -389.7163378  1.6545        -388.0618092  2.7305        -390.7922733  21.534  19.914   2.842  51.028
   7     -390.7922733 0.68551        -390.1067664 0.32480E-01    -390.1392465  10.688  10.427   3.424  42.350
   8     -390.1392465 0.65858E-01    -390.0733882  2.7839        -392.8573233  21.807  21.131   7.872  18.420
   1     -392.8573233  7.3210        -385.5363475 0.29176        -385.8281028  26.397  24.279   2.371  61.166
   4     -385.8281028  1.7269        -384.1011549  1.0124        -385.1135753  23.366  20.221   4.995  29.026
   6     -385.1135753 0.10959        -385.0039875 0.25254        -385.2565250   8.289   8.207   3.597  40.311
   2     -385.2565250 0.41198        -384.8445499  1.4451        -386.2896343   6.553   5.627   8.005  18.114

 Number of TS in the path       =      7
 Number of cycles               =      5

 Elapsed time=                                96.22
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             38382 time=          48.98 %= 50.9
 OPTIM> # of energy+gradient+Hessian calls=       435 time=           1.57 %=  1.6
