
============ PROCESS INFORMATION =============
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 ### CCP4 8.0.010: Refmac          version 5.8.0405 : 02/05/23##
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 User: flong  Run date:  3/ 4/2023 Run time: 00:01:02 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- ligand
  Data line--- ncyc 10
  Data line--- make hout yes
  Data line--- make hydr full
  Data line--- chir 4
  Data line--- END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - Test_ORN_TMP/mol_1_conf_1_tmp_init.pdb
Output coordinate file. Logical name - XYZOUT actual file name - Test_ORN_TMP/mol_1_conf_1_tmp_refmac_stage_0.pdb

  Refinement type                        : Idealisation

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /Users/flong/CCP4/ccp4-8.0/lib/data/monomers/mon*cif
Parameters for neW entry and VDW: /Users/flong/CCP4/ccp4-8.0/lib/data/monomers/ener_lib.cif
User supplied dictionary entries: Test_ORN_TMP/Test_ORN_mol_0_cod.rst
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will be generated with full occupancies
    hydrogens will be written to the output file
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Method of minimisation                 : Sparse Matrix

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 4.00

 NON-BONDED CONTACTS
          Overall weight                          =  2.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------

 Input file :Test_ORN_TMP/mol_1_conf_1_tmp_init.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         ?
 _lib_version      ?
 _lib_update       ?
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :     3
                with complete description    :     3
  NUMBER OF MODIFICATIONS                    :   119
  NUMBER OF LINKS                            :    97
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  WARNING: "SCALE" card is absent in input PDB file
  set_mod
  Number of atoms    :       9
  Number of residues :       1
  Number of chains   :       1
 ---------
  I am reading library. Please wait.
                mon_lib.cif


                ******Default connectivity*******


                    **** Automatic generation of links ****

   Link info given in this sectoion is for information only
   If you want to use this links then either add them into the pdb/mmcif file or use make link yes option

  In create description
  --------------------------------
  --- title of input coord file ---

  PDB_code:  OR
  PDB_name:UNL
  PDB_date:03/04/202
  --------------------------------
  WARNING : ORN      X1   1 X1_   : unknown chemical type of atom NE   - N32
                  default type is - "N   "
  Number of chains                  :       1
  Total number of monomers          :       1
  Number of atoms                   :      21
  Number of missing atoms           :       0
  Number of rebuilt atoms           :      12
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
  In create description
  --------------------------------
  --- title of input coord file ---

  PDB_code:OR
  PDB_name:UNL
  PDB_date:03-JAN-02
  --------------------------------
  WARNING : ORN      X1   1 X1_   : unknown chemical type of atom NE   - N32
                  default type is - "N   "
  Number of chains                  :       1
  Total number of monomers          :       1
  Number of atoms                   :      21
  Number of missing atoms           :       0
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :      20
  Number of angles restraints   :      36
  Number of torsions restraints :       6
  Number of chiralities         :       1
  Number of planar groups       :       1

 Scattering factors file : /Users/flong/CCP4/ccp4-8.0/lib/data/atomsf.lib


_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N+1   12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  O-1    4.1952  12.8573   1.6411   4.1724   1.5281  47.0179 -20.3246  -0.0140  21.9602
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:        20         0        20
               Angles:        36         0        36
              Chirals:         1         0         1
               Planes:         1         0         1
             Torsions:         6         0         6
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


   Current auto weighting coefficient =    4.00000000    



     CGMAT cycle number =        1

    ****                          Bond angle outliers                           ****

Bond angle deviations from the ideal >10.000Sigma will be monitored

X      1 ORN HE1   - X      1 ORN HE2   mod.= 141.30 id.= 108.08 dev=-33.220 sig.=  3.000

 function value    147.056473    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.052     0.015
Bond distances: others                           12     0.001     0.016
Bond angles  : refined atoms                      9     3.042     2.296
Bond angles  : others                            27     6.487     2.380
Chiral centres: refined atoms                     1     0.209     0.200
Planar groups: refined atoms                      4     0.001     0.020
VDW repulsions.others                             4     0.181     0.200
VDW; torsion: refined_atoms                       2     0.075     0.200
VDW; torsion.others                               4     0.183     0.200
-------------------------------------------------------------------------------
 iters           62   4.10816446E-02   1.73009699E-03   42.1128883       4.10823632E-05
 Not converging with gamma equal    0.00000000    
 Trying gamma equal    5.24999984E-02   0.00000000    
 Gamma decreased to    4.19999994E-02
  Iterations           47
 average, maximum and rms of positional shifts    4.43649106E-03  0.145065680       3.62457298E-02
   147.056473       1.40129846E-45   1.00000000       1.00000000     T
 fvalues    0.00000000       147.056473       147.056473       1.00000003E+32


     CGMAT cycle number =        2

 function value    32.8624496    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.005     0.015
Bond distances: others                           12     0.006     0.016
-------------------------------------------------------------------------------
 Gamma decreased to    3.24545428E-02
  Iterations           57
 average, maximum and rms of positional shifts   -9.51540016E-04   6.89398050E-02   1.36638721E-02
   32.8624496       147.056473       1.00000000       1.00000000     F
 fvalues    0.00000000       32.8624496       32.8624496       147.056473    


     CGMAT cycle number =        3

 function value    30.1202698    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.004     0.015
Bond distances: others                           12     0.001     0.016
-------------------------------------------------------------------------------
 Gamma decreased to    2.37768572E-02
  Iterations           62
 average, maximum and rms of positional shifts   -1.53192796E-03   8.31550881E-02   1.69576816E-02
   30.1202698       32.8624496       1.00000000       1.00000000     F
 fvalues    0.00000000       30.1202698       30.1202698       32.8624496    


     CGMAT cycle number =        4

 function value    26.7071800    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.004     0.015
Bond distances: others                           12     0.003     0.016
-------------------------------------------------------------------------------
 Gamma decreased to    1.58880539E-02
  Iterations           67
 average, maximum and rms of positional shifts   -6.91267755E-03  0.305503845       6.35387897E-02
   26.7071800       30.1202698       1.00000000       1.00000000     F
 fvalues    0.00000000       26.7071800       26.7071800       30.1202698    


     CGMAT cycle number =        5

 function value    66.0662994    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.006     0.015
Bond distances: others                           12     0.054     0.016
-------------------------------------------------------------------------------
 Gamma decreased to    8.71641375E-03
  Iterations           62
 average, maximum and rms of positional shifts    2.62940465E-03   9.69265401E-02   1.83929112E-02
   66.0662994       26.7071800      0.618034005      0.618034005     T
 fvalues    0.00000000       66.0662994       66.0662994       26.7071800    


     CGMAT cycle number =        6

 function value    17.7878304    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.004     0.015
Bond distances: others                           12     0.023     0.016
-------------------------------------------------------------------------------
 Gamma decreased to    2.19674082E-03
  Iterations           72
 average, maximum and rms of positional shifts    1.77490490E-03   4.92420606E-02   1.76214632E-02
   17.7878304       66.0662994      0.618034005      0.618034005     F
 fvalues    0.00000000       17.7878304       17.7878304       66.0662994    


     CGMAT cycle number =        7

 function value    9.20196342    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.004     0.015
Bond distances: others                           12     0.009     0.016
-------------------------------------------------------------------------------
 Gamma decreased to    0.00000000    
  Iterations          108
 average, maximum and rms of positional shifts    7.68789556E-03  0.207969368       6.97346330E-02
   9.20196342       17.7878304       1.00000000       1.00000000     F
 fvalues    0.00000000       9.20196342       9.20196342       17.7878304    


     CGMAT cycle number =        8

 function value    16.8829288    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.005     0.015
Bond distances: others                           12     0.015     0.016
-------------------------------------------------------------------------------
 iters           72   4.04327147E-04   1.68038932E-05   13.4389381       1.25038844E-06
 Not converging with gamma equal    0.00000000    
 Trying gamma equal    2.82878354E-02   0.00000000    
 Gamma decreased to    2.26302687E-02
  Iterations           60
 average, maximum and rms of positional shifts    3.73139716E-04   2.79016308E-02   6.48882892E-03
   16.8829288       9.20196342      0.618034005      0.618034005     T
 fvalues    0.00000000       16.8829288       16.8829288       9.20196342    


     CGMAT cycle number =        9

 function value    6.32101536    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.003     0.015
Bond distances: others                           12     0.006     0.016
-------------------------------------------------------------------------------
 Gamma decreased to    1.74870268E-02
  Iterations           66
 average, maximum and rms of positional shifts    3.23399145E-04   2.58669723E-02   6.61524944E-03
   6.32101536       16.8829288      0.618034005      0.618034005     F
 fvalues    0.00000000       6.32101536       6.32101536       16.8829288    


     CGMAT cycle number =       10

 function value    4.46212101    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                     8     0.003     0.015
Bond distances: others                           12     0.002     0.016
Bond angles  : refined atoms                      9     0.921     2.296
Bond angles  : others                            27     0.403     2.380
Chiral centres: refined atoms                     1     0.024     0.200
Planar groups: refined atoms                      4     0.001     0.020
VDW repulsions.others                             2     0.068     0.200
VDW; torsion: refined_atoms                       1     0.139     0.200
VDW; torsion.others                               4     0.077     0.200
-------------------------------------------------------------------------------
 Gamma decreased to    1.28113516E-02
  Iterations           72
 average, maximum and rms of positional shifts    5.71430486E-04   4.57705930E-02   1.28286378E-02
   4.46212101       6.32101536       1.00000000       1.00000000     F
 fvalues    0.00000000       4.46212101       4.46212101       6.32101536    
  Time in seconds: CPU =         0.02
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.0      0.0      0.0             0.       0.0   0.0515  2.980   3.042  1.863   0.209
       1   0.0      0.0      0.0             0.       0.0   0.0049  0.349   1.310  0.539   0.061
       2   0.0      0.0      0.0             0.       0.0   0.0041  0.347   1.276  0.496   0.036
       3   0.0      0.0      0.0             0.       0.0   0.0041  0.344   1.338  0.509   0.033
       4   0.0      0.0      0.0             0.       0.0   0.0058  0.393   1.379  0.521   0.032
       5   0.0      0.0      0.0             0.       0.0   0.0044  0.335   1.375  0.521   0.032
       6   0.0      0.0      0.0             0.       0.0   0.0038  0.302   1.310  0.503   0.034
       7   0.0      0.0      0.0             0.       0.0   0.0047  0.318   0.889  0.387   0.036
       8   0.0      0.0      0.0             0.       0.0   0.0032  0.245   0.902  0.379   0.028
       9   0.0      0.0      0.0             0.       0.0   0.0027  0.221   0.921  0.377   0.024
 $$
 $TEXT:Result: $$ Final results $$
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
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 Refmac:  End of Refmac_5.8.0405   
Times: User:       0.8s System:    0.0s Elapsed:     0:01  
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=========END OF PROCESS INFORMATION
 ==========
