
 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)@comp20.ch.
                 Created on  5/28/12 at 13:12:13 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=    -390.7173267     RMS force=    0.9395562145E-06
 OPTIM> Final energy  =    -389.2134661     RMS force=    0.9364700186E-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=     3564.9    
 decide> The unconnected minima in the chain and their distances are:
     2       15.28     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1207 Dev= 0.53% S= 15.90 time= 0.75
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   5.97

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     958 steps. Energy=    -389.2134661       time=       3.06
 Minus side of path:                     991 steps. Energy=    -390.6863946       time=       4.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2134661 0.39690         -388.8165691  1.8698         -390.6863946  13.373  11.770   2.527  57.390
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     305.97    
 decide> The unconnected minima in the chain and their distances are:
     3        6.74     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2205 Dev= 0.82% S= 7.20 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   6.42

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     978 steps. Energy=    -390.7072739       time=       3.62
 Minus side of path:                     925 steps. Energy=    -390.7173267       time=       3.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7072739 0.88728E-02     -390.6984010 0.18926E-01     -390.7173267   0.936   0.928   3.358  43.187
        *NEW* (Placed in 4)                                     Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     252.24    
 decide> The unconnected minima in the chain and their distances are:
     3        6.32     4 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 4_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 2.9559 Dev= 2.94% S= 6.91 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.86

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     968 steps. Energy=    -390.6062077       time=       2.69
 Minus side of path:                     952 steps. Energy=    -390.6863946       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.6062077 0.26694E-01     -390.5795138 0.10688         -390.6863946   3.436   3.417   2.746  52.795
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     451.75    
 decide> The unconnected minima in the chain and their distances are:
     5        7.67     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S 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= 0.2681 Dev= 0.43% S= 8.10 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   6.15

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     978 steps. Energy=    -390.6227560       time=       4.28
 Minus side of path:                     980 steps. Energy=    -390.7072739       time=       4.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.6227560 0.22615E-01     -390.6001407 0.10713         -390.7072739   3.241   3.226   2.776  52.240
        *NEW* (Placed in 6)                                     Known (#4)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     268.15    
 decide> The unconnected minima in the chain and their distances are:
     5        6.45     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3264 Dev= 0.91% S= 6.95 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   6.48
 isnewts> transition state is the same as number        4 energy=     -390.6001407367
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     969 steps. Energy=    -390.6227560       time=       2.36
 Minus side of path:                     971 steps. Energy=    -390.7072739       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.6227560 0.22615E-01     -390.6001407 0.10713         -390.7072739   3.241   3.226   2.776  52.241
        Known (#6)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     297.95    
 decide> The unconnected minima in the chain and their distances are:
     3        6.68     6 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 6_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.3433 Dev= 0.24% S= 7.13 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   4.09
 isnewts> transition state is the same as number        4 energy=     -390.6001407357
 tryconnect> Will not repeat search for TS      1 same as TS      4
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     504.48    
 decide> The unconnected minima in the chain and their distances are:
     3        6.32     4 
 

 tryconnect> 490-iteration DNEB run for minima 3_F and 4_S using 14 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0090 Dev= 1.91% S= 9.35 time= 8.96
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.91

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     985 steps. Energy=    -390.6863946       time=       2.56
 Minus side of path:                     990 steps. Energy=    -390.7072739       time=       2.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.6863946  2.8929         -387.7934962  2.9138         -390.7072739   7.255   6.320  25.181   5.758
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -390.7173267 0.18926E-01    -390.6984010 0.88728E-02    -390.7072739   0.936   0.928   3.358  43.187
   6     -390.7072739  2.9138        -387.7934962  2.8929        -390.6863946   7.255   6.320  25.181   5.758
   1     -390.6863946  1.8698        -388.8165691 0.39690        -389.2134661  13.373  11.770   2.527  57.390

 Number of TS in the path       =      3
 Number of cycles               =      7

 Elapsed time=                                87.92
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             26690 time=          33.51 %= 38.1
 OPTIM> # of energy+gradient+Hessian calls=       254 time=           1.40 %=  1.6
