
 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)@comp34.ch.
                 Created on  5/28/12 at 10:37:11 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=    -385.1178926     RMS force=    0.9454601519E-06
 OPTIM> Final energy  =    -381.3066617     RMS force=    0.9731877753E-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      80.49430856    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.29993E+06
 decide> The unconnected minima in the chain and their distances are:
     2       66.86     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=     0
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step   1174 fraction=    0.990000 images=     7 time=       1.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1199 steps, energy/image=     2448.338500     RMS=20.14476102     images=   8
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   73.65     Attempts, images and iterations=     0    22   770
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 770 RMS= 0.0332 Dev= 4.74% S= 83.93 time= 20.52
 Following    2 images are candidates for TS:    3   17  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=  22.96

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1044 steps. Energy=    -380.0181651       time=       2.93
 Minus side of path:                    1023 steps. Energy=    -381.3066617       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.0181651 0.11328         -379.9048874  1.4018         -381.3066617  24.600  22.281   1.875  77.322
        *NEW* (Placed in 3)                                     Known (#2)
 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=    0.15165E+06
 decide> The unconnected minima in the chain and their distances are:
     3       53.27     1 
 

 tryconnect> Interpolation for minima 1_S and 3_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=     1
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    587 fraction=    0.990000 images=     5 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    612 steps, energy/image=    -132.0790422     RMS=11.99948072     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   55.78     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.2017697586    
 Double-ended search iterations= 560 RMS= 0.0976 Dev= 6.05% S= 62.61 time= 10.84
 Following    2 images are candidates for TS:    4   13  
 Converged to TS (number of iterations):        206
 Converged to TS (number of iterations):         84
 DNEB run yielded 2 true transition state(s) time=  20.06

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1216 steps. Energy=    -385.1178926       time=       3.27
 Minus side of path:                     937 steps. Energy=    -380.9785863       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1178926  4.4106         -380.7072506 0.27134         -380.9785863  29.352  25.437   1.908  76.003
        Known (#1)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    80   91 from     0.33263E-01 to     0.42781E-01 ref=     2.4230    
 checkperc> Increasing con cutoff atoms    80   92 from     0.70714E-01 to     0.86624E-01 ref=     2.5160    
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1300 steps. Energy=    -381.5678225       time=       3.59
 Minus side of path:                    1000 steps. Energy=    -380.0181651       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5678225  1.5614         -380.0064347 0.11730E-01     -380.0181651  43.281  41.956   1.784  81.297
        *NEW* (Placed in 5)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    68   70 from     0.44717E-02 to     0.45401E-02 ref=    0.98276    
 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      4 steps with      1 missing connections, weight=     13147.    
 decide> The unconnected minima in the chain and their distances are:
     5       23.58     4 
 

 tryconnect> Interpolation for minima 4_S and 5_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=    24
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    176 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    201 steps, energy/image=    -279.8313666     RMS=16.53390861     images=   4
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   30.39     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.5098621309    
 Double-ended search iterations= 315 RMS= 0.2480 Dev= 1.26% S= 26.33 time= 3.50
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         39
 Converged to TS (number of iterations):         55
 DNEB run yielded 2 true transition state(s) time=   8.98

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     976 steps. Energy=    -380.9785863       time=       2.19
 Minus side of path:                    1312 steps. Energy=    -387.3512235       time=       3.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.9785863 0.93813         -380.0404571  7.3108         -387.3512235  35.185  31.993   2.736  53.001
        Known (#4)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1015 steps. Energy=    -381.5678225       time=       2.29
 Minus side of path:                    1409 steps. Energy=    -387.3512235       time=       4.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5678225 0.95206         -380.6157663  6.7355         -387.3512235  38.002  23.982   1.945  74.542
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -385.1178926  4.4106        -380.7072506 0.27134        -380.9785863  29.352  25.437   1.908  76.003
   4     -380.9785863 0.93813        -380.0404571  7.3108        -387.3512235  35.185  31.993   2.736  53.001
   5     -387.3512235  6.7355        -380.6157663 0.95206        -381.5678225  38.002  23.982   1.945  74.542
   3     -381.5678225  1.5614        -380.0064347 0.11730E-01    -380.0181651  43.281  41.956   1.784  81.297
   1     -380.0181651 0.11328        -379.9048874  1.4018        -381.3066617  24.600  22.281   1.875  77.322

 Number of TS in the path       =      5
 Number of cycles               =      3

 Elapsed time=                               119.17
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             47433 time=          55.37 %= 46.5
 OPTIM> # of energy+gradient+Hessian calls=       700 time=           2.74 %=  2.3
