
 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> Constraint potential parameters read from file congeom.dat
 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)@comp31.ch.
                 Created on  5/28/12 at 10:37:26 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -382.6517516     RMS force=    0.9790532668E-06
 OPTIM> Final energy  =    -379.3011876     RMS force=    0.9720334003E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      38.30043642    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     55397.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.08     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    17
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    298 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    323 steps, energy/image=    -361.6523883     RMS=1.855453483     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   40.09     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0682 Dev= 2.94% S= 45.46 time= 5.84
 Following    2 images are candidates for TS:    1   10  
 Converged to TS (number of iterations):         21
 Converged to TS (number of iterations):         48
 DNEB run yielded 2 true transition state(s) time=   9.67

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     993 steps. Energy=    -384.0989856       time=       2.54
 Minus side of path:                    1022 steps. Energy=    -382.6517516       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0989856  1.8185         -382.2804784 0.37127         -382.6517516  12.146  11.826   1.975  73.400
        *NEW* (Placed in 3)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    65   70 from     0.94185E-01 to     0.98880E-01 ref=     2.6336    
 checkperc> Increasing con cutoff atoms    66   69 from     0.11906E-01 to     0.13392E-01 ref=     1.9735    
 checkperc> Increasing con cutoff atoms    67   68 from     0.19858E-01 to     0.25023E-01 ref=     2.1927    
 checkperc> Increasing con cutoff atoms    67   69 from     0.48122E-01 to     0.65974E-01 ref=     2.3551    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1009 steps. Energy=    -381.7644736       time=       2.44
 Minus side of path:                    1021 steps. Energy=    -380.2155834       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7644736  2.4603         -379.3041634 0.91142         -380.2155834  14.441  13.904   2.915  49.739
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     42246.    
 decide> The unconnected minima in the chain and their distances are:
     2       13.09     4     5       34.16     1 
 

 tryconnect> Interpolation for minima 2_F and 4_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   115
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     31 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     56 steps, energy/image=    -373.9464612     RMS=.3145030478     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   18.82     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 175 RMS= 0.2448 Dev= 0.56% S= 13.21 time= 1.00
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   4.89
 isnewts> transition state is the same as number        2 energy=     -379.3041634428
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1022 steps. Energy=    -381.7644736       time=       2.42
 Minus side of path:                    1036 steps. Energy=    -380.2155834       time=       2.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7644736  2.4603         -379.3041634 0.91142         -380.2155834  14.441  13.904   2.909  49.853
        Known (#4)                                              Known (#5)
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S and 5_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    14
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    156 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    181 steps, energy/image=    -369.3825930     RMS=.5572165775     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      1     5 dist=   36.04     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.2722 Dev= 0.81% S= 37.17 time= 4.01
 Following    2 images are candidates for TS:    2    9  
 Converged to TS (number of iterations):         29
 Converged to TS (number of iterations):         76
 DNEB run yielded 2 true transition state(s) time=   9.65
 isnewts> transition state is the same as number        1 energy=     -382.2804783998
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1002 steps. Energy=    -384.0989856       time=       2.20
 Minus side of path:                     995 steps. Energy=    -382.6517516       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0989856  1.8185         -382.2804784 0.37127         -382.6517516  12.146  11.826   1.976  73.379
        Known (#3)                                              Known (#1)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1142 steps. Energy=    -383.4268737       time=       2.74
 Minus side of path:                    1015 steps. Energy=    -380.2155834       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4268737  3.2179         -380.2089945 0.65889E-02     -380.2155834  29.558  28.787   2.248  64.492
        *NEW* (Placed in 6)                                     Known (#5)
 checkperc> Increasing con cutoff atoms   120  121 from     0.60051E-02 to     0.61084E-02 ref=     1.3731    
 checkperc> Increasing con cutoff atoms   121  127 from     0.62028E-02 to     0.62107E-02 ref=     2.4054    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     7343.3    
 decide> The unconnected minima in the chain and their distances are:
     2       13.09     4     6       14.15     1 
 

 tryconnect> Interpolation for minima 2_F and 4_U using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   115
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     35 fraction=    0.990000 images=    15 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     60 steps, energy/image=    -331.8898038     RMS=17.82104736     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   21.11     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 805 RMS= 0.0831 Dev= 11.68% S= 18.68 time= 20.83
 Following    2 images are candidates for TS:    5   12  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         25
 DNEB run yielded 2 true transition state(s) time=   6.48
 isnewts> transition state is the same as number        2 energy=     -379.3041634428
 tryconnect> Will not repeat search for TS      2 same as TS      2

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1068 steps. Energy=    -380.2155834       time=       2.41
 Minus side of path:                    1003 steps. Energy=    -379.3011876       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834 0.93079         -379.2847946 0.16393E-01     -379.3011876  20.327  18.831   2.176  66.633
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 6_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    93
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     57 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     82 steps, energy/image=    -363.4224993     RMS=9.348994694     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      1     6 dist=   19.73     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 175 RMS= 0.0646 Dev= 0.49% S= 14.37 time= 1.00
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   4.74

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1011 steps. Energy=    -383.4268737       time=       2.20
 Minus side of path:                    1031 steps. Energy=    -381.8353908       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4268737  2.2710         -381.1559056 0.67949         -381.8353908  15.642  13.201   2.357  61.511
        Known (#6)                                              *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms   125  126 from     0.54755E-02 to     0.68739E-02 ref=    0.98443    
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     105.66    
 decide> The unconnected minima in the chain and their distances are:
     7        4.72     1 
 

 tryconnect> Interpolation for minima 1_S and 7_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   144
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -377.8609382     RMS=1.380908155     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      1     7 dist=   12.52     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 105 RMS= 0.0820 Dev= 0.85% S= 4.73 time= 0.36
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1030 steps. Energy=    -382.6517516       time=       2.26
 Minus side of path:                     974 steps. Energy=    -381.8353908       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6517516 0.81700         -381.8347519 0.63893E-03     -381.8353908   4.763   4.723   3.588  40.416
        Known (#1)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -382.6517516 0.81700        -381.8347519 0.63893E-03    -381.8353908   4.763   4.723   3.588  40.416
   7     -381.8353908 0.67949        -381.1559056  2.2710        -383.4268737  15.642  13.201   2.357  61.511
   5     -383.4268737  3.2179        -380.2089945 0.65889E-02    -380.2155834  29.558  28.787   2.248  64.492
   6     -380.2155834 0.93079        -379.2847946 0.16393E-01    -379.3011876  20.327  18.831   2.176  66.633

 Number of TS in the path       =      4
 Number of cycles               =      4

 Elapsed time=                               112.10
 OPTIM> # of energy calls=                         12 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             55617 time=          60.51 %= 54.0
 OPTIM> # of energy+gradient+Hessian calls=       355 time=           1.27 %=  1.1
