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 ### CCP4 8.0.007: Refmac          version 5.8.0403 : 11/30/22##
 ###############################################################
 User: unknown  Run date: 21/12/2022 Run time: 13:04:27 


 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.


 $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--- make     check NONE
  Data line--- refi     type REST reso 47.32 2.10     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 5
  Data line--- ncyc 10
  Data line--- weight matrix 0.0600
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: poli67_1-9A.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - poli_ccp4sw2023_R00_2-30A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli_ccp4sw2023_R00_2-10A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli_ccp4sw2023_R00_2-10A.mtz

Cell from mtz :    58.265    79.758    94.643    90.000    90.000    90.000
Space group from mtz: number -   19; name - P 21 21 21

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /opt/ccp4/ccp4-8.0/lib/data/monomers/mon*cif
Parameters for neW entry and VDW: /opt/ccp4/ccp4-8.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    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


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     5       0.0454
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  2.1000
  Estimated number of reflections :      34260
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.0600
  Refinement cycles       :         10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    47.3245  2.1000

  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= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          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

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 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
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :poli_ccp4sw2023_R00_2-30A.pdb
  NUMBER OF MONOMERS IN THE LIBRARY          : 35279
                with complete description    : 35279
  NUMBER OF MODIFICATIONS                    :   119
  NUMBER OF LINKS                            :    98
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  set_mod
  Number of atoms    :    2286
  Number of residues :     307
  Number of chains   :       3
 ---------
  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:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  A1_  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  A1_  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  B2_  is missing in the structure
  ATTENTION: atom:OXT  THR                70  B2_  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  B2_  is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     307
  Number of atoms                   :    4696
  Number of missing atoms           :       5
  Number of rebuilt atoms           :    2331
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
  In create description
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  A1_  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  A1_  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  B2_  is missing in the structure
  ATTENTION: atom:OXT  THR                70  B2_  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  B2_  is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     307
  Number of atoms                   :    4696
  Number of missing atoms           :       5
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :    4571
  Number of angles restraints   :    8304
  Number of torsions restraints :    2161
  Number of chiralities         :     329
  Number of planar groups       :     746

 Scattering factors file : /opt/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     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
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0317


 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:      4571         0      4571
               Angles:      8304         0      8304
              Chirals:       329         0       329
               Planes:       746         0       746
             Torsions:      2161         0      2161
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections       1283
Number of   all  reflections      26407
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          26407

   Current auto weighting coefficient =    7.74955940    



######  TLS Group Definitions ######



     CGMAT cycle number =        1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Weight matrix    5.99999987E-02
 Actual weight    23.8534813      is applied to the X-ray term
Norm of X_ray positional gradient                40.1
Norm of Geom. positional gradient                85.2
Norm of X_ray B-factor gradient                  47.1
Norm of Geom. B-factor gradient                  24.0
Product of X_ray and Geom posit. gradients     -0.156E+08
 Cosine of angle between them                      -0.333
Product of X_ray and Geom B-fact gradients     -0.359E+07
 Cosine of angle between them                      -0.693


Residuals: XRAY=     0.2527E+07 GEOM=     0.1252E+05 TOTAL=     0.2540E+07
 function value    2540014.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.017     0.012
Bond distances: others                         2287     0.002     0.016
Bond angles  : refined atoms                   3054     1.858     1.652
Bond angles  : others                          5250     0.896     1.577
Torsion angles, period  1. refined              265     7.195     5.000
Torsion angles, period  2. refined               19     1.538     5.000
Torsion angles, period  3. refined              475    21.320    10.000
Torsion angles, period  6. refined              116    16.895    10.000
Chiral centres: refined atoms                   329     0.077     0.200
Planar groups: refined atoms                   2643     0.009     0.020
Planar groups: others                           553     0.011     0.020
VDW repulsions: refined_atoms                   507     0.222     0.200
VDW repulsions.others                          1922     0.211     0.200
VDW; torsion: refined_atoms                    1091     0.171     0.200
VDW; torsion.others                            1236     0.079     0.200
HBOND: refined_atoms                             50     0.175     0.200
VDW repulsions: symmetry: refined_atoms          10     0.147     0.200
VDW repulsions: symmetry: others                 30     0.268     0.200
HBOND: symmetry: refined_atoms                    3     0.135     0.200
M. chain bond B values: refined atoms          1075     7.318     7.057
M. chain bond B values: others                 1075     7.298     7.056
M. chain angle B values: refined atoms         1335     9.833    12.701
M. chain angle B values: others                1336     9.833    12.709
S. chain bond B values: refined atoms          1209     8.646     7.896
S. chain bond B values: others                 1210     8.642     7.899
S. chain angle B values: refined atoms         1719    12.333    14.170
S. chain angle B values: others                1720    12.329    14.173
Long range B values: refined atoms             2586    14.521    67.752
Long range B values: others                    2586    14.533    67.770
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5332, B  =    0.1974
Partial structure    1: scale =     0.3834, B  =   54.3986
Overall anisotropic scale factors
   B11 =   5.60 B22 =  -1.82 B33 =  -3.78 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   275.0   273.9  0.21  0.22     116   256.6   259.1  0.34  0.34
 0.068    4157  99.86   173.6   162.4  0.20  0.19     220   174.6   162.7  0.25  0.24
 0.114    5265  99.71    67.5    62.6  0.24  0.21     282    66.1    63.1  0.33  0.30
 0.159    6203  99.89    32.7    32.0  0.33  0.29     319    34.6    34.7  0.37  0.33
 0.204    7017  99.95    21.9    16.9  0.43  0.43     344    21.3    16.1  0.44  0.44
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.807    567   0.737   2431   0.790  0.910  0.9304  0.9701  0.8357  0.9227
  0.0683   3575   0.834    582   0.743   4157   0.821  0.997  0.9570  0.9766  0.8530  0.9266
  0.1136   4683   0.754    582   0.675   5265   0.745  0.947  0.9273  0.9626  0.7484  0.8970
  0.1589   5624   0.577    579   0.533   6203   0.573  0.736  0.8980  0.9078  0.7354  0.8232
  0.2041   6433   0.234    589   0.211   7022   0.232  0.356  0.7026  0.7064  0.6822  0.6369
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2382
Free R factor                        =     0.3154
Average Fourier shell correlation    =     0.8804
AverageFree Fourier shell correlation=     0.8650
Overall weighted R factor            =     0.2158
Free weighted R factor               =     0.2948
Overall weighted R2 factor           =     0.2345
Free weighted R2 factor              =     0.3231
Average correlation coefficient      =     0.8133
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9127
Cruickshanks DPI for coordinate error=     0.1928
DPI based on free R factor           =     0.2034
Overall figure of merit              =     0.5760
ML based su of positional parameters =     0.2645
ML based su of thermal parameters    =    11.7260
-----------------------------------------------------------------------------
 iters          800   1.34938375E-07   2.21781349E-09  0.588959277       3.76564824E-09
 Not converging with gamma equal    0.00000000    
 Trying gamma equal    5.24999984E-02   0.00000000    
 Gamma decreased to    4.19999994E-02
  Iterations           67
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -6.17928919E-04  0.252437383       1.75159685E-02
   2540014.25       0.00000000       1.00000000       1.00000000     T
 fvalues    105959.211       12518.2773       2540014.25       1.00000003E+32


     CGMAT cycle number =        2

 Weight matrix    5.99999987E-02
 Actual weight    21.9207230      is applied to the X-ray term


 function value    2330463.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5202, B  =   -0.4515
Partial structure    1: scale =     0.3853, B  =   55.2669
Overall anisotropic scale factors
   B11 =   5.38 B22 =  -1.71 B33 =  -3.67 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2355
Free R factor                        =     0.3121
Average Fourier shell correlation    =     0.8822
AverageFree Fourier shell correlation=     0.8655
Average correlation coefficient      =     0.8162
Overall figure of merit              =     0.5856
-----------------------------------------------------------------------------
 Gamma decreased to    3.24545428E-02
  Iterations           79
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -4.22406651E-04  0.199808240       1.19673489E-02
   2330463.00       2540014.25       1.00000000       1.00000000     F
 fvalues    105823.758       10729.8564       2330463.00       2540014.25    


     CGMAT cycle number =        3

 Weight matrix    5.99999987E-02
 Actual weight    21.6483307      is applied to the X-ray term


 function value    2301292.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5185, B  =   -0.0470
Partial structure    1: scale =     0.3862, B  =   55.3574
Overall anisotropic scale factors
   B11 =   5.31 B22 =  -1.66 B33 =  -3.65 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2342
Free R factor                        =     0.3113
Average Fourier shell correlation    =     0.8830
AverageFree Fourier shell correlation=     0.8654
Average correlation coefficient      =     0.8181
Overall figure of merit              =     0.5868
-----------------------------------------------------------------------------
 Gamma decreased to    2.37768572E-02
  Iterations           90
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -2.51815334E-04  0.187505126       1.13975126E-02
   2301292.25       2330463.00       1.00000000       1.00000000     F
 fvalues    105798.258       10936.5254       2301292.25       2330463.00    


     CGMAT cycle number =        4

 Weight matrix    6.00000024E-02
 Actual weight    21.6456299      is applied to the X-ray term


 function value    2302519.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5129, B  =   -0.2081
Partial structure    1: scale =     0.3893, B  =   56.1020
Overall anisotropic scale factors
   B11 =   5.26 B22 =  -1.63 B33 =  -3.62 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2334
Free R factor                        =     0.3115
Average Fourier shell correlation    =     0.8839
AverageFree Fourier shell correlation=     0.8658
Average correlation coefficient      =     0.8190
Overall figure of merit              =     0.5871
-----------------------------------------------------------------------------
 Gamma decreased to    1.58880539E-02
  Iterations          105
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -2.38754074E-04  0.182517067       1.20501658E-02
   2302519.75       2301292.25       1.00000000       1.00000000     F
 fvalues    105861.617       11078.2881       2302519.75       2301292.25    


     CGMAT cycle number =        5

 Weight matrix    5.99999949E-02
 Actual weight    21.6597443      is applied to the X-ray term


 function value    2304894.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5103, B  =   -0.0493
Partial structure    1: scale =     0.3923, B  =   56.5480
Overall anisotropic scale factors
   B11 =   5.22 B22 =  -1.60 B33 =  -3.62 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2331
Free R factor                        =     0.3110
Average Fourier shell correlation    =     0.8844
AverageFree Fourier shell correlation=     0.8660
Average correlation coefficient      =     0.8198
Overall figure of merit              =     0.5867
-----------------------------------------------------------------------------
 Gamma decreased to    8.71641375E-03
  Iterations          128
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.10115659E-04  0.118905604       8.62874836E-03
   2304894.50       2302519.75      0.618034005      0.618034005     T
 fvalues    105896.648       11200.2031       2304894.50       2302519.75    


     CGMAT cycle number =        6

 Weight matrix    5.99999949E-02
 Actual weight    21.7008514      is applied to the X-ray term


 function value    2309574.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5093, B  =   -0.0387
Partial structure    1: scale =     0.3929, B  =   56.6511
Overall anisotropic scale factors
   B11 =   5.21 B22 =  -1.60 B33 =  -3.61 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2330
Free R factor                        =     0.3105
Average Fourier shell correlation    =     0.8845
AverageFree Fourier shell correlation=     0.8661
Average correlation coefficient      =     0.8198
Overall figure of merit              =     0.5866
-----------------------------------------------------------------------------
 Gamma decreased to    2.19674082E-03
  Iterations          172
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -4.40607691E-05  0.100825675       7.34879775E-03
   2309574.25       2304894.50      0.381966025      0.381966025     T
 fvalues    105909.578       11246.1387       2309574.25       2304894.50    


     CGMAT cycle number =        7

 Weight matrix    5.99999949E-02
 Actual weight    21.9202728      is applied to the X-ray term


 function value    2333097.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5098, B  =   -0.0149
Partial structure    1: scale =     0.3955, B  =   57.3021
Overall anisotropic scale factors
   B11 =   5.19 B22 =  -1.58 B33 =  -3.60 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2327
Free R factor                        =     0.3104
Average Fourier shell correlation    =     0.8851
AverageFree Fourier shell correlation=     0.8667
Average correlation coefficient      =     0.8201
Overall figure of merit              =     0.5837
-----------------------------------------------------------------------------
 Gamma decreased to    0.00000000    
  Iterations          354
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts    4.05641076E-05  0.113035716       8.49143136E-03
   2333097.50       2309574.25      0.236067981      0.236067981     T
 fvalues    105921.469       11270.0820       2333097.50       2309574.25    


     CGMAT cycle number =        8

 Weight matrix    5.99999987E-02
 Actual weight    21.6866474      is applied to the X-ray term


 function value    2307003.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5116, B  =    0.0306
Partial structure    1: scale =     0.3960, B  =   57.5138
Overall anisotropic scale factors
   B11 =   5.18 B22 =  -1.58 B33 =  -3.60 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2325
Free R factor                        =     0.3106
Average Fourier shell correlation    =     0.8848
AverageFree Fourier shell correlation=     0.8662
Average correlation coefficient      =     0.8202
Overall figure of merit              =     0.5869
-----------------------------------------------------------------------------
 iters          800   5.14521794E-08   2.07773176E-09  0.332751572       6.24409280E-09
 Not converging with gamma equal    0.00000000    
 Trying gamma equal    2.82878354E-02   0.00000000    
 Gamma decreased to    2.26302687E-02
  Iterations           96
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -2.16889821E-05   3.78043465E-02   1.92753202E-03
   2307003.25       2333097.50      0.236067981      0.236067981     F
 fvalues    105858.383       11289.6436       2307003.25       2333097.50    


     CGMAT cycle number =        9

 Weight matrix    5.99999949E-02
 Actual weight    21.9335461      is applied to the X-ray term


 function value    2333567.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5123, B  =    0.0349
Partial structure    1: scale =     0.3965, B  =   57.7002
Overall anisotropic scale factors
   B11 =   5.18 B22 =  -1.58 B33 =  -3.59 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2324
Free R factor                        =     0.3107
Average Fourier shell correlation    =     0.8852
AverageFree Fourier shell correlation=     0.8666
Average correlation coefficient      =     0.8202
Overall figure of merit              =     0.5837
-----------------------------------------------------------------------------
 Gamma decreased to    1.74870268E-02
  Iterations          107
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.10119463E-05   3.79069969E-02   1.90820755E-03
   2333567.50       2307003.25      0.200000003      0.200000003     T
 fvalues    105877.648       11295.1953       2333567.50       2307003.25    


     CGMAT cycle number =       10

 Weight matrix    5.99999987E-02
 Actual weight    21.6980515      is applied to the X-ray term


 function value    2308318.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5116, B  =    0.0019
Partial structure    1: scale =     0.3967, B  =   57.7587
Overall anisotropic scale factors
   B11 =   5.16 B22 =  -1.58 B33 =  -3.59 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2325
Free R factor                        =     0.3110
Average Fourier shell correlation    =     0.8849
AverageFree Fourier shell correlation=     0.8663
Average correlation coefficient      =     0.8201
Overall figure of merit              =     0.5872
-----------------------------------------------------------------------------
 Gamma decreased to    1.28113516E-02
  Iterations          122
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.50426640E-05   4.35441099E-02   2.23416043E-03
   2308318.50       2333567.50      0.200000003      0.200000003     F
 fvalues    105862.406       11310.4434       2308318.50       2333567.50    

 LABOUT FreeR_flag=FreeR_flag F_XDSdataset=F_XDSdataset SIGF_XDSdataset=SIGF_XDSdataset FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: poli_ccp4sw2023_R00_2-10A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.010     0.012
Bond distances: others                         2287     0.001     0.016
Bond angles  : refined atoms                   3054     1.966     1.652
Bond angles  : others                          5250     0.605     1.577
Torsion angles, period  1. refined              265     7.444     5.000
Torsion angles, period  2. refined               19     9.052     5.000
Torsion angles, period  3. refined              475    20.717    10.000
Torsion angles, period  6. refined              116    15.584    10.000
Chiral centres: refined atoms                   329     0.083     0.200
Planar groups: refined atoms                   2643     0.010     0.020
Planar groups: others                           553     0.001     0.020
VDW repulsions: refined_atoms                   554     0.249     0.200
VDW repulsions.others                          2158     0.199     0.200
VDW; torsion: refined_atoms                    1120     0.193     0.200
VDW; torsion.others                            1350     0.087     0.200
HBOND: refined_atoms                             56     0.199     0.200
VDW repulsions: symmetry: refined_atoms           8     0.189     0.200
VDW repulsions: symmetry: others                 36     0.210     0.200
HBOND: symmetry: refined_atoms                    3     0.153     0.200
M. chain bond B values: refined atoms          1075     8.390     6.910
M. chain bond B values: others                 1075     8.348     6.907
M. chain angle B values: refined atoms         1335    10.581    12.357
M. chain angle B values: others                1336    10.585    12.365
S. chain bond B values: refined atoms          1209     9.963     7.730
S. chain bond B values: others                 1210     9.959     7.733
S. chain angle B values: refined atoms         1719    13.856    13.836
S. chain angle B values: others                1720    13.852    13.839
Long range B values: refined atoms             2664    15.441    65.986
Long range B values: others                    2664    15.446    66.005
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5116, B  =    0.0007
Partial structure    1: scale =     0.3967, B  =   57.7644
Overall anisotropic scale factors
   B11 =   5.16 B22 =  -1.58 B33 =  -3.59 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   279.0   277.6  0.21  0.21     116   260.2   261.0  0.33  0.33
 0.068    4157  99.86   176.1   164.3  0.19  0.18     220   177.1   163.5  0.25  0.24
 0.114    5265  99.71    68.5    63.8  0.24  0.21     282    67.0    63.9  0.33  0.30
 0.159    6203  99.89    33.2    32.6  0.32  0.29     319    35.1    35.2  0.37  0.33
 0.204    7017  99.95    22.2    17.2  0.42  0.41     344    21.6    16.3  0.42  0.42
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.830    567   0.757   2431   0.813  0.916  0.9323  0.9724  0.8348  0.9304
  0.0683   3575   0.834    582   0.745   4157   0.821  0.998  0.9569  0.9781  0.8530  0.9313
  0.1136   4683   0.764    582   0.689   5265   0.756  0.952  0.9290  0.9645  0.7596  0.8983
  0.1589   5624   0.572    579   0.531   6203   0.568  0.732  0.8973  0.9119  0.7294  0.8253
  0.2041   6433   0.251    589   0.231   7022   0.250  0.377  0.7080  0.7173  0.6904  0.6533
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2325
Free R factor                        =     0.3108
Average Fourier shell correlation    =     0.8853
AverageFree Fourier shell correlation=     0.8668
Overall weighted R factor            =     0.2105
Free weighted R factor               =     0.2894
Overall weighted R2 factor           =     0.2287
Free weighted R2 factor              =     0.3205
Average correlation coefficient      =     0.8202
Overall correlation coefficient      =     0.9608
Free correlation coefficient         =     0.9124
Cruickshanks DPI for coordinate error=     0.1881
DPI based on free R factor           =     0.2005
Overall figure of merit              =     0.5840
ML based su of positional parameters =     0.2521
ML based su of thermal parameters    =    11.1634
-----------------------------------------------------------------------------
  Time in seconds: CPU =         8.93
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2382   0.3154   0.576      105959.    5553.9   0.0169  1.532   1.858  1.123   0.077
       1   0.2355   0.3121   0.586      105824.    5558.7   0.0111  0.911   1.861  1.109   0.079
       2   0.2342   0.3113   0.587      105798.    5559.7   0.0106  0.860   1.894  1.122   0.082
       3   0.2334   0.3115   0.587      105862.    5564.1   0.0105  0.847   1.918  1.131   0.082
       4   0.2331   0.3110   0.587      105897.    5567.0   0.0104  0.843   1.939  1.140   0.082
       5   0.2330   0.3105   0.587      105910.    5567.3   0.0104  0.842   1.949  1.144   0.082
       6   0.2327   0.3104   0.584      105921.    5567.8   0.0104  0.841   1.955  1.146   0.083
       7   0.2325   0.3106   0.587      105858.    5565.3   0.0104  0.842   1.960  1.149   0.083
       8   0.2324   0.3107   0.584      105878.    5566.1   0.0104  0.842   1.961  1.149   0.083
       9   0.2325   0.3110   0.587      105862.    5566.0   0.0104  0.842   1.964  1.150   0.083
      10   0.2325   0.3108   0.584      105886.    5566.7   0.0104  0.842   1.966  1.151   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2382   0.2325
             R free    0.3154   0.3108
     Rms BondLength    0.0169   0.0104
      Rms BondAngle    1.8582   1.9656
     Rms ChirVolume    0.0773   0.0828
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0403   
Times: User:      13.1s System:    0.1s Elapsed:     0:13