
 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)@comp35.ch.
                 Created on  5/28/12 at 11:36:12 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


 natintsetup, NATOMS           79
 cartres            7
 KeyInt>> Using natural internal coordinates. # of coords =        231
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         44      2388
 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -292.4977479     RMS force=    0.7278454191E-06
 OPTIM> Final energy  =    -292.6004611     RMS force=    0.9191864151E-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=     36514.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.18     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0982 Dev= 2.75% S= 40.39 time= 1.57
 Following    3 images are candidates for TS:    4    6    9  
 Converged to TS (number of iterations):         52
 Converged to TS (number of iterations):         28
 Converged to TS (number of iterations):         16
 DNEB run yielded 3 true transition state(s) time=   2.32

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     533 steps. Energy=    -291.3677259       time=       0.41
 Minus side of path:                     732 steps. Energy=    -291.8130375       time=       0.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3677259  2.0503         -289.3174165  2.4956         -291.8130375  22.183  18.963   1.895  41.694
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     526 steps. Energy=    -291.3731350       time=       0.43
 Minus side of path:                     547 steps. Energy=    -292.6896602       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3731350 0.42122         -290.9519108  1.7377         -292.6896602  13.185  13.029   1.970  40.095
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     494 steps. Energy=    -292.6004611       time=       0.39
 Minus side of path:                     514 steps. Energy=    -292.6896602       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.6004611 0.32705         -292.2734132 0.41625         -292.6896602   7.548   7.257   2.519  31.364
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1214.6    
 decide> The unconnected minima in the chain and their distances are:
     5       10.31     4     3        4.93     1 
 

 tryconnect> 105-iteration DNEB run for minima 4_U and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5685 Dev= 0.73% S= 12.47 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   1.10

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     531 steps. Energy=    -291.3987611       time=       0.41
 Minus side of path:                     679 steps. Energy=    -297.3730826       time=       0.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3987611 0.16919         -291.2295736  6.1435         -297.3730826  16.747  15.569   1.947  40.577
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 3.1546 Dev= 0.51% S= 5.41 time= 0.10
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   1.10

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     517 steps. Energy=    -291.3677259       time=       0.40
 Minus side of path:                     525 steps. Energy=    -291.2555284       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3677259 0.14548         -291.2222453 0.33283E-01     -291.2555284   3.928   3.846  18.029   4.382
        Known (#3)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     2429.1    
 decide> The unconnected minima in the chain and their distances are:
     5       10.31     4     3        4.93     1 
 

 tryconnect> 805-iteration DNEB run for minima 4_U and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 805 RMS= 0.0673 Dev= 4.03% S= 18.36 time= 9.74
 Following    2 images are candidates for TS:    9   20  
 Converged to TS (number of iterations):         11
 Converged to TS (number of iterations):         22
 DNEB run yielded 2 true transition state(s) time=   1.14
 isnewts> transition state is the same as number        4 energy=     -291.2295735807
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     603 steps. Energy=    -291.8130375       time=       0.49
 Minus side of path:                     820 steps. Energy=    -297.3730826       time=       0.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.8130375  4.3531         -287.4599451  9.9131         -297.3730826  24.403  21.686   2.883  27.405
        Known (#4)                                              Known (#8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     526 steps. Energy=    -291.3987611       time=       0.41
 Minus side of path:                     683 steps. Energy=    -297.3730826       time=       0.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3987611 0.16919         -291.2295736  6.1435         -297.3730826  16.744  15.568   1.942  40.675
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 3_U using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0113 Dev= 4.96% S= 6.76 time= 2.24
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   0.49

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     544 steps. Energy=    -291.3677259       time=       0.43
 Minus side of path:                     521 steps. Energy=    -292.4977479       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3677259  2.2573         -289.1104409  3.3873         -292.4977479   5.369   4.933  17.948   4.402
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1070.6    
 decide> The unconnected minima in the chain and their distances are:
     5       10.23     7 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0491 Dev= 0.01% S= 10.27 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   0.52

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     515 steps. Energy=    -291.3987611       time=       0.39
 Minus side of path:                     499 steps. Energy=    -291.3731350       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3987611 0.25397         -291.1447931 0.22834         -291.3731350  10.284  10.230   2.101  37.597
        Known (#7)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -292.4977479  3.3873        -289.1104409  2.2573        -291.3677259   5.369   4.933  17.948   4.402
   1     -291.3677259  2.0503        -289.3174165  2.4956        -291.8130375  22.183  18.963   1.895  41.694
   6     -291.8130375  4.3531        -287.4599451  9.9131        -297.3730826  24.403  21.686   2.883  27.405
   4     -297.3730826  6.1435        -291.2295736 0.16919        -291.3987611  16.747  15.569   1.947  40.577
   9     -291.3987611 0.25397        -291.1447931 0.22834        -291.3731350  10.284  10.230   2.101  37.597
   2     -291.3731350 0.42122        -290.9519108  1.7377        -292.6896602  13.185  13.029   1.970  40.095
   3     -292.6896602 0.41625        -292.2734132 0.32705        -292.6004611   7.548   7.257   2.519  31.364

 Number of TS in the path       =      7
 Number of cycles               =      4

 Elapsed time=                                29.49
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41784 time=          20.71 %= 70.2
 OPTIM> # of energy+gradient+Hessian calls=       270 time=           0.27 %=  0.9
