
 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 12:20:21 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.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -288.5233623     RMS force=    0.9929384981E-06
 OPTIM> Final energy  =    -288.3199581     RMS force=    0.9685577300E-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=     778.20    
 decide> The unconnected minima in the chain and their distances are:
     2        9.20     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 1.4391 Dev= 1.27% S= 14.24 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   0.72

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     467 steps. Energy=    -292.4752365       time=       0.37
 Minus side of path:                     477 steps. Energy=    -293.9333040       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.4752365  2.0655         -290.4097423  3.5236         -293.9333040   4.623   4.083  24.284   3.253
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1556.4    
 decide> The unconnected minima in the chain and their distances are:
     2        9.20     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 2_F using 21 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 735 RMS= 0.6468 Dev= 5.67% S= 26.76 time= 8.74
 Following    4 images are candidates for TS:    5   10   14   17  
 Converged to TS (number of iterations):         45
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):         31
 Converged to TS (number of iterations):         38
 DNEB run yielded 4 true transition state(s) time=   3.04

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     521 steps. Energy=    -290.6403572       time=       0.42
 Minus side of path:                     504 steps. Energy=    -286.9299015       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.6403572  5.2759         -285.3645008  1.5654         -286.9299015   8.024   7.170   9.666   8.173
        *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:                     512 steps. Energy=    -290.6403572       time=       0.41
 Minus side of path:                     506 steps. Energy=    -291.3357850       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.6403572  3.7459         -286.8944190  4.4414         -291.3357850  11.316   6.875  10.057   7.855
        Known (#5)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     484 steps. Energy=    -290.8684196       time=       0.39
 Minus side of path:                     468 steps. Energy=    -293.9669114       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.8684196  1.5904         -289.2780235  4.6889         -293.9669114   5.664   5.085  15.886   4.973
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     474 steps. Energy=    -292.4752365       time=       0.38
 Minus side of path:                     508 steps. Energy=    -290.3356707       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.4752365  3.1975         -289.2777539  1.0579         -290.3356707   9.109   8.696   5.467  14.451
        Known (#3)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 10 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      4 missing connections, weight=     1409.3    
 decide> The unconnected minima in the chain and their distances are:
     2        7.71     3     4        2.72     9     8        4.33     7     6        9.47     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4422 Dev= 1.85% S= 8.16 time= 0.09
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   0.57

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     487 steps. Energy=    -288.3199581       time=       0.39
 Minus side of path:                     490 steps. Energy=    -292.4752365       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.3199581 0.68071         -287.6392499  4.8360         -292.4752365   8.336   7.717  14.579   5.419
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_F and 9_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0989 Dev= 0.08% S= 2.89 time= 0.09
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   0.46

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     458 steps. Energy=    -293.9333040       time=       0.36
 Minus side of path:                     451 steps. Energy=    -293.9669114       time=       0.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.9333040 0.96914         -292.9641667  1.0027         -293.9669114   2.885   2.720  28.000   2.821
        Known (#4)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 8_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0946 Dev= 0.13% S= 4.38 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   0.76

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     481 steps. Energy=    -290.3310724       time=       0.38
 Minus side of path:                     494 steps. Energy=    -291.3357850       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.3310724 0.74396E-01     -290.2566763  1.0791         -291.3357850   3.382   3.193  13.742   5.749
        *NEW* (Placed in 11)                                    Known (#7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.5809 Dev= 0.55% S= 10.01 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   0.74

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     542 steps. Energy=    -286.9299015       time=       0.44
 Minus side of path:                     522 steps. Energy=    -287.6052936       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -286.9299015  2.7192         -284.2106628  3.3946         -287.6052936  10.337   9.006  13.723   5.757
        Known (#6)                                              *NEW* (Placed in 12)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      2 missing connections, weight=     414.43    
 decide> The unconnected minima in the chain and their distances are:
     8        3.95    11    12        7.07     1 
 

 tryconnect> 70-iteration DNEB run for minima 8_F and 11_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0375 Dev= 0.08% S= 3.96 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.54

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     483 steps. Energy=    -290.8684196       time=       0.39
 Minus side of path:                     462 steps. Energy=    -290.3310724       time=       0.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.8684196 0.65377         -290.2146508 0.11642         -290.3310724   3.971   3.946   9.892   7.986
        Known (#8)                                              Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 12_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5406 Dev= 0.34% S= 7.20 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   0.71

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     506 steps. Energy=    -287.6052936       time=       0.41
 Minus side of path:                     526 steps. Energy=    -288.5233623       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.6052936 0.27890         -287.3263972  1.1970         -288.5233623   7.979   7.070   6.004  13.158
        Known (#12)                                             Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  11     -288.5233623  1.1970        -287.3263972 0.27890        -287.6052936   7.979   7.070   6.004  13.158
   9     -287.6052936  3.3946        -284.2106628  2.7192        -286.9299015  10.337   9.006  13.723   5.757
   2     -286.9299015  1.5654        -285.3645008  5.2759        -290.6403572   8.024   7.170   9.666   8.173
   3     -290.6403572  3.7459        -286.8944190  4.4414        -291.3357850  11.316   6.875  10.057   7.855
   8     -291.3357850  1.0791        -290.2566763 0.74396E-01    -290.3310724   3.382   3.193  13.742   5.749
  10     -290.3310724 0.11642        -290.2146508 0.65377        -290.8684196   3.971   3.946   9.892   7.986
   4     -290.8684196  1.5904        -289.2780235  4.6889        -293.9669114   5.664   5.085  15.886   4.973
   7     -293.9669114  1.0027        -292.9641667 0.96914        -293.9333040   2.885   2.720  28.000   2.821
   1     -293.9333040  3.5236        -290.4097423  2.0655        -292.4752365   4.623   4.083  24.284   3.253
   6     -292.4752365  4.8360        -287.6392499 0.68071        -288.3199581   8.336   7.717  14.579   5.419

 Number of TS in the path       =     10
 Number of cycles               =      4

 Elapsed time=                                26.21
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             32821 time=          17.58 %= 67.1
 OPTIM> # of energy+gradient+Hessian calls=       280 time=           0.30 %=  1.1
