
 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     79
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     8
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 11:58:15 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> *
 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

  
 CHARMM>    BOMLev -5
 MISCOM> Setting BOMLev < -2 is NOT a good idea.
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 2
 Parameter: 0 <- "/HOME/BS360/C31A2-SAT39/TOPPAR"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp::
 OPNLGU> Unit  1 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp
 MAINIO> Residue topology file being read from unit   1.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * ALSO, TOPOLOGY FOR D-PROLINE (DPR) RESIDUE WAS ADDED.
 TITLE> * * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
 TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
 TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
 TITLE> *
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp::
 OPNLGU> Unit  2 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> * - PARAMETER FILE PARAM19 * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 VCLOSE: Closing unit    2 with status "KEEP"
 MAINIO> Sequence information being read from unit   5.
 RDTITL> *

          RESIDUE SEQUENCE --     7 RESIDUES
          GLY ASN ASN GLN GLN ASN TYR 
 THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is SEG1.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        7
         Number of atoms         =       79   Number of groups     =       33
         Number of bonds         =       79   Number of angles     =      113
         Number of dihedrals     =       48   Number of impropers  =       37
         Number of cross-terms   =        0
         Number of HB acceptors  =       14   Number of HB donors  =       20
         Number of NB exclusions =        3   Total charge =    0.00000
 VOPEN> Attempting to open::input.crd::
 OPNLGU> Unit 20 opened for READONLY access to input.crd
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> 79
 VCLOSE: Closing unit   20 with status "KEEP"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      GROUps   RDIElec  SWITch   VGROup   VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 15.000 CTEXNB =999.000 CTONNB =  7.000 CTOFNB =  9.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found    195 exclusions and    129 interactions(1-4)
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/solvpar.inp::
 OPNLGU> Unit 30 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/solvpar.inp
 NBOND           79
 NTHETA          113
 NPHI           48

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           14
 chsetdihe> NOMEGAC            6
 chsetdihe> NSIDECHAIN           15
 chsetdihe> NCHIRAL            6

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            14
 chsetdihe> NOMEGACTOT=             6
 chsetdihe> NSIDECHAINTOT=            15
 chsetdihe> NCHIRALTOT=             6

 chsetdihe>            29  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1      79

 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>  237 Cartesian coordinates will be optimised for   79 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -292.6953475     RMS force=    0.7586990566E-06
 OPTIM> Final energy  =    -288.7793570     RMS force=    0.8048701049E-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=     21079.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.62     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 1.1574 Dev= 1.53% S= 32.83 time= 1.26
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   1.22

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     536 steps. Energy=    -290.1908647       time=       0.42
 Minus side of path:                     535 steps. Energy=    -288.7793570       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.1908647  4.2804         -285.9104248  2.8689         -288.7793570  10.392   9.502   6.742  11.718
        *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=     23429.    
 decide> The unconnected minima in the chain and their distances are:
     3       28.61     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1976 Dev= 0.90% S= 33.34 time= 1.26
 Following    3 images are candidates for TS:    3    5    8  
 Converged to TS (number of iterations):        179
 Converged to TS (number of iterations):         41
 Converged to TS (number of iterations):         26
 DNEB run yielded 3 true transition state(s) time=   5.02

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     543 steps. Energy=    -298.1633820       time=       0.45
 Minus side of path:                     488 steps. Energy=    -292.6953475       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -298.1633820  5.4849         -292.6784463 0.16901E-01     -292.6953475   7.667   7.551   2.857  27.649
        *NEW* (Placed in 4)                                     Known (#1)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     723 steps. Energy=    -295.7417854       time=       0.68
 Minus side of path:                     683 steps. Energy=    -291.6986588       time=       0.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.7417854  7.7083         -288.0334500  3.6652         -291.6986588  21.655  11.981   4.154  19.018
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     508 steps. Energy=    -290.1908647       time=       0.40
 Minus side of path:                     536 steps. Energy=    -292.2817711       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.1908647 0.15536         -290.0355042  2.2463         -292.2817711   6.799   6.184   7.341  10.762
        Known (#3)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     12049.    
 decide> The unconnected minima in the chain and their distances are:
     7       21.49     6     5       12.84     4 
 

 tryconnect> 210-iteration DNEB run for minima 6_U and 7_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.8194 Dev= 1.43% S= 23.07 time= 0.73
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   0.80

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     530 steps. Energy=    -292.9759077       time=       0.45
 Minus side of path:                     533 steps. Energy=    -291.6986588       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.9759077  3.8873         -289.0885845  2.6101         -291.6986588   8.475   7.945   3.252  24.289
        *NEW* (Placed in 8)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_S and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 107 RMS= 0.3851 Dev= 0.64% S= 13.13 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   0.80

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     536 steps. Energy=    -295.7417854       time=       0.45
 Minus side of path:                     522 steps. Energy=    -298.1633820       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.7417854  3.4614         -292.2803578  5.8830         -298.1633820  13.976  12.866   3.333  23.699
        Known (#5)                                              Known (#4)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     6960.7    
 decide> The unconnected minima in the chain and their distances are:
     7       19.09     8 
 

 tryconnect> 175-iteration DNEB run for minima 7_F and 8_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1057 Dev= 0.15% S= 19.49 time= 0.51
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   0.74

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     519 steps. Energy=    -291.9754406       time=       0.44
 Minus side of path:                     512 steps. Energy=    -292.2817711       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.9754406  1.2014         -290.7739983  1.5078         -292.2817711  18.436  18.250   2.373  33.295
        *NEW* (Placed in 9)                                     Known (#7)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     133.11    
 decide> The unconnected minima in the chain and their distances are:
     9        5.11     8 
 

 tryconnect> 70-iteration DNEB run for minima 8_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1180 Dev= 0.45% S= 5.16 time= 0.08
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.56

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     492 steps. Energy=    -291.9754406       time=       0.43
 Minus side of path:                     528 steps. Energy=    -292.9759077       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.9754406 0.70765E-01     -291.9046759  1.0712         -292.9759077   5.437   5.107   3.085  25.612
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -292.6953475 0.16901E-01    -292.6784463  5.4849        -298.1633820   7.667   7.551   2.857  27.649
   6     -298.1633820  5.8830        -292.2803578  3.4614        -295.7417854  13.976  12.866   3.333  23.699
   3     -295.7417854  7.7083        -288.0334500  3.6652        -291.6986588  21.655  11.981   4.154  19.018
   5     -291.6986588  2.6101        -289.0885845  3.8873        -292.9759077   8.475   7.945   3.252  24.289
   8     -292.9759077  1.0712        -291.9046759 0.70765E-01    -291.9754406   5.437   5.107   3.085  25.612
   7     -291.9754406  1.2014        -290.7739983  1.5078        -292.2817711  18.436  18.250   2.373  33.295
   4     -292.2817711  2.2463        -290.0355042 0.15536        -290.1908647   6.799   6.184   7.341  10.762
   1     -290.1908647  4.2804        -285.9104248  2.8689        -288.7793570  10.392   9.502   6.742  11.718

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                                20.86
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             21069 time=          11.36 %= 54.4
 OPTIM> # of energy+gradient+Hessian calls=       427 time=           0.47 %=  2.3
