
 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)@comp35.ch.
                 Created on  5/28/12 at 10:32:41 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=    -385.6672879     RMS force=    0.9212940466E-06
 OPTIM> Final energy  =    -390.4661157     RMS force=    0.9841990842E-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      14.39580941    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1820.5    
 decide> The unconnected minima in the chain and their distances are:
     2       12.20     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=   112
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    100 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    125 steps, energy/image=    -378.3227281     RMS=.5022209802     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   14.47     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1977 Dev= 1.47% S= 14.24 time= 0.68
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   5.44

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     945 steps. Energy=    -385.6672879       time=       2.25
 Minus side of path:                     953 steps. Energy=    -388.7845356       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.6672879 0.96803         -384.6992617  4.0853         -388.7845356  10.271   9.104   2.845  50.970
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     332.28    
 decide> The unconnected minima in the chain and their distances are:
     2        6.92     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S 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=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     42 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     67 steps, energy/image=    -384.3929577     RMS=.3788324944     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   8.634     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2370 Dev= 0.86% S= 7.36 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.24

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     948 steps. Energy=    -388.7845356       time=       2.82
 Minus side of path:                     954 steps. Energy=    -390.1025028       time=       3.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7845356  2.3814         -386.4031828  3.6993         -390.1025028   9.264   7.802  19.334   7.500
        Known (#3)                                              *NEW* (Placed in 4)
 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=     152.88    
 decide> The unconnected minima in the chain and their distances are:
     2        5.34     4 
 

 tryconnect> Interpolation for minima 2_F and 4_S 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=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     27 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     52 steps, energy/image=    -386.0556862     RMS=.3320162558     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   6.137     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.2578 Dev= 1.33% S= 5.64 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        139
 DNEB run yielded 1 true transition state(s) time=  12.72

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1134 steps. Energy=    -390.4661157       time=       3.52
 Minus side of path:                     992 steps. Energy=    -387.4832740       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4661157  3.3056         -387.1605044 0.32277         -387.4832740  36.693  35.129   4.124  35.162
        Known (#2)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms     9   13 from     0.13584E-01 to     0.14225E-01 ref=     2.4473    
 checkperc> Increasing con cutoff atoms    39   40 from     0.23076E-02 to     0.31595E-02 ref=     1.5253    
 checkperc> Increasing con cutoff atoms    39   42 from     0.76667E-02 to     0.93886E-02 ref=     3.6267    
 checkperc> Increasing con cutoff atoms    40   42 from     0.20607E-02 to     0.27918E-02 ref=     2.1258    
 checkperc> Increasing con cutoff atoms    40   44 from     0.74166E-03 to     0.77104E-03 ref=     1.3809    
 checkperc> Increasing con cutoff atoms    40   45 from     0.16331E-02 to     0.34735E-02 ref=     2.1596    
 checkperc> Increasing con cutoff atoms    41   44 from     0.18040E-02 to     0.18971E-02 ref=     2.2652    
 checkperc> Increasing con cutoff atoms    60   64 from     0.17241E-01 to     0.21240E-01 ref=     2.4492    
 checkperc> Increasing con cutoff atoms    62   63 from     0.49763E-02 to     0.57374E-02 ref=    0.98236    
 checkperc> Increasing con cutoff atoms    64   74 from     0.11452     to     0.11533     ref=     2.5362    
 checkperc> Increasing con cutoff atoms    72   73 from     0.25948E-01 to     0.29492E-01 ref=     2.2547    
 checkperc> Increasing con cutoff atoms    72   75 from     0.67402E-01 to     0.76014E-01 ref=     2.8163    
 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      3 steps with      1 missing connections, weight=     305.76    
 decide> The unconnected minima in the chain and their distances are:
     2        5.34     4 
 

 tryconnect> Interpolation for minima 2_F and 4_S 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=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     30 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     55 steps, energy/image=    -386.2551211     RMS=.2819868578     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   7.190     Attempts, images and iterations=     1    16   560
 lbfgs> Final DNEB force constant     0.2224511589    
 Double-ended search iterations= 560 RMS= 0.0093 Dev= 3.32% S= 7.52 time= 11.07
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.46

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     953 steps. Energy=    -390.1025028       time=       3.37
 Minus side of path:                     942 steps. Energy=    -390.4661157       time=       3.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1025028  2.2584         -387.8441406  2.6220         -390.4661157   6.241   5.343  24.259   5.977
        Known (#4)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -385.6672879 0.96803        -384.6992617  4.0853        -388.7845356  10.271   9.104   2.845  50.970
   2     -388.7845356  2.3814        -386.4031828  3.6993        -390.1025028   9.264   7.802  19.334   7.500
   4     -390.1025028  2.2584        -387.8441406  2.6220        -390.4661157   6.241   5.343  24.259   5.977

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                                62.77
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             22344 time=          26.96 %= 43.0
 OPTIM> # of energy+gradient+Hessian calls=       222 time=           1.09 %=  1.7
