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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: 13:05:37 


 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 1.90     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_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli_ccp4sw2023_R00_1-90A.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_1-90A.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       0.0554
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  1.9000
  Estimated number of reflections :      45570
  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  1.9000

  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_2-00A.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       1724
Number of   all  reflections      35468
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          35468

   Current auto weighting coefficient =    7.25002575    



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



     CGMAT cycle number =        1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Weight matrix    6.00000024E-02
 Actual weight    22.5845890      is applied to the X-ray term
Norm of X_ray positional gradient                35.1
Norm of Geom. positional gradient                47.5
Norm of X_ray B-factor gradient                  35.8
Norm of Geom. B-factor gradient                  32.7
Product of X_ray and Geom posit. gradients     -0.169E+08
 Cosine of angle between them                      -0.738
Product of X_ray and Geom B-fact gradients     -0.322E+07
 Cosine of angle between them                      -0.601


Residuals: XRAY=     0.2990E+07 GEOM=     0.1382E+05 TOTAL=     0.3004E+07
 function value    3004217.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.011     0.012
Bond distances: others                         2287     0.002     0.016
Bond angles  : refined atoms                   3054     2.064     1.652
Bond angles  : others                          5250     1.014     1.577
Torsion angles, period  1. refined              265     7.614     5.000
Torsion angles, period  2. refined               19    10.502     5.000
Torsion angles, period  3. refined              475    20.820    10.000
Torsion angles, period  6. refined              116    15.740    10.000
Chiral centres: refined atoms                   329     0.086     0.200
Planar groups: refined atoms                   2643     0.011     0.020
Planar groups: others                           553     0.014     0.020
VDW repulsions: refined_atoms                   570     0.254     0.200
VDW repulsions.others                          2162     0.226     0.200
VDW; torsion: refined_atoms                    1135     0.194     0.200
VDW; torsion.others                            1351     0.091     0.200
HBOND: refined_atoms                             59     0.203     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           7     0.202     0.200
VDW repulsions: symmetry: others                 39     0.249     0.200
HBOND: symmetry: refined_atoms                    3     0.137     0.200
M. chain bond B values: refined atoms          1075     8.780     6.818
M. chain bond B values: others                 1075     8.762     6.816
M. chain angle B values: refined atoms         1335    11.010    12.184
M. chain angle B values: others                1336    11.007    12.192
S. chain bond B values: refined atoms          1209    10.399     7.676
S. chain bond B values: others                 1210    10.395     7.679
S. chain angle B values: refined atoms         1719    14.390    13.707
S. chain angle B values: others                1720    14.386    13.710
Long range B values: refined atoms             2690    16.048    65.138
Long range B values: others                    2689    16.058    65.154
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4603, B  =   -1.2376
Partial structure    1: scale =     0.3868, B  =   56.3179
Overall anisotropic scale factors
   B11 =   4.69 B22 =  -1.44 B33 =  -3.25 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   276.8   273.7  0.20  0.20     153   263.7   259.5  0.29  0.29
 0.083    5552  99.88   137.2   125.0  0.20  0.19     305   136.6   125.9  0.28  0.26
 0.139    7124  99.77    45.7    47.1  0.28  0.24     364    47.4    50.4  0.36  0.32
 0.194    8355  99.91    24.8    22.2  0.39  0.38     424    24.7    22.1  0.41  0.40
 0.249    8476  89.91    19.7    10.1  0.55  0.55     428    20.3    10.5  0.54  0.53
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.819    698   0.751   3240   0.804  0.932  0.9416  0.9737  0.8494  0.9289
  0.0834   4838   0.800    714   0.710   5552   0.788  1.001  0.9493  0.9748  0.8576  0.9353
  0.1387   6411   0.655    713   0.607   7124   0.650  0.788  0.9172  0.9495  0.7134  0.8723
  0.1940   7643   0.442    712   0.388   8355   0.437  0.592  0.8389  0.8476  0.6957  0.7041
  0.2493   7833   0.389    643   0.383   8476   0.388  0.800  0.8357  0.7986  0.4101  0.4559
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2537
Free R factor                        =     0.3260
Average Fourier shell correlation    =     0.8911
AverageFree Fourier shell correlation=     0.8846
Overall weighted R factor            =     0.2200
Free weighted R factor               =     0.2954
Overall weighted R2 factor           =     0.2282
Free weighted R2 factor              =     0.3160
Average correlation coefficient      =     0.7379
Overall correlation coefficient      =     0.9619
Free correlation coefficient         =     0.9207
Cruickshanks DPI for coordinate error=     0.1541
DPI based on free R factor           =     0.1681
Overall figure of merit              =     0.5666
ML based su of positional parameters =     0.2572
ML based su of thermal parameters    =    10.4318
-----------------------------------------------------------------------------
 iters          800   8.38050127E-08   2.82711055E-09  0.417657286       6.76897205E-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   -2.29740021E-04  0.172707453       1.05307028E-02
   3004217.00       4.55884429E-41   1.00000000       1.00000000     T
 fvalues    132408.703       13820.6836       3004217.00       1.00000003E+32


     CGMAT cycle number =        2

 Weight matrix    6.00000024E-02
 Actual weight    21.8734646      is applied to the X-ray term


 function value    2904583.00    

-------------------------------------------------------------------------------
             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 =     1.4580, B  =   -0.3682
Partial structure    1: scale =     0.3867, B  =   55.3408
Overall anisotropic scale factors
   B11 =   4.70 B22 =  -1.45 B33 =  -3.25 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2543
Free R factor                        =     0.3245
Average Fourier shell correlation    =     0.8800
AverageFree Fourier shell correlation=     0.8722
Average correlation coefficient      =     0.7423
Overall figure of merit              =     0.5551
-----------------------------------------------------------------------------
 Gamma decreased to    3.24545428E-02
  Iterations           78
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts    1.52336452E-05  0.184386238       8.06806330E-03
   2904583.00       3004217.00       1.00000000       1.00000000     F
 fvalues    132244.547       11936.4043       2904583.00       3004217.00    


     CGMAT cycle number =        3

 Weight matrix    5.99999949E-02
 Actual weight    22.0474701      is applied to the X-ray term


 function value    2927283.50    

-------------------------------------------------------------------------------
             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 =     1.4589, B  =   -0.0787
Partial structure    1: scale =     0.3867, B  =   55.4921
Overall anisotropic scale factors
   B11 =   4.71 B22 =  -1.46 B33 =  -3.25 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2543
Free R factor                        =     0.3258
Average Fourier shell correlation    =     0.8800
AverageFree Fourier shell correlation=     0.8716
Average correlation coefficient      =     0.7427
Overall figure of merit              =     0.5534
-----------------------------------------------------------------------------
 Gamma decreased to    2.37768572E-02
  Iterations           90
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -4.45588157E-05  0.130173609       5.33214491E-03
   2927283.50       2904583.00      0.618034005      0.618034005     T
 fvalues    132217.500       12221.9580       2927283.50       2904583.00    


     CGMAT cycle number =        4

 Weight matrix    5.99999949E-02
 Actual weight    21.8810692      is applied to the X-ray term


 function value    2904408.75    

-------------------------------------------------------------------------------
             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 =     1.4606, B  =   -0.0505
Partial structure    1: scale =     0.3868, B  =   55.5689
Overall anisotropic scale factors
   B11 =   4.71 B22 =  -1.45 B33 =  -3.26 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2543
Free R factor                        =     0.3260
Average Fourier shell correlation    =     0.8806
AverageFree Fourier shell correlation=     0.8720
Average correlation coefficient      =     0.7431
Overall figure of merit              =     0.5553
-----------------------------------------------------------------------------
 Gamma decreased to    1.58880539E-02
  Iterations          106
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.74302022E-05  0.133594811       6.05916418E-03
   2904408.75       2927283.50      0.618034005      0.618034005     F
 fvalues    132179.922       12170.7715       2904408.75       2927283.50    


     CGMAT cycle number =        5

 Weight matrix    5.99999949E-02
 Actual weight    22.0585499      is applied to the X-ray term


 function value    2928336.00    

-------------------------------------------------------------------------------
             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 =     1.4598, B  =   -0.0854
Partial structure    1: scale =     0.3866, B  =   55.5777
Overall anisotropic scale factors
   B11 =   4.71 B22 =  -1.45 B33 =  -3.26 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3260
Average Fourier shell correlation    =     0.8804
AverageFree Fourier shell correlation=     0.8717
Average correlation coefficient      =     0.7434
Overall figure of merit              =     0.5539
-----------------------------------------------------------------------------
 Gamma decreased to    8.71641375E-03
  Iterations          129
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -8.54669997E-06   8.42218995E-02   4.60540364E-03
   2928336.00       2904408.75      0.381966025      0.381966025     T
 fvalues    132203.281       12123.1758       2928336.00       2904408.75    


     CGMAT cycle number =        6

 Weight matrix    5.99999987E-02
 Actual weight    21.9710426      is applied to the X-ray term


 function value    2917061.25    

-------------------------------------------------------------------------------
             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 =     1.4593, B  =   -0.1059
Partial structure    1: scale =     0.3867, B  =   55.6844
Overall anisotropic scale factors
   B11 =   4.71 B22 =  -1.45 B33 =  -3.25 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3262
Average Fourier shell correlation    =     0.8808
AverageFree Fourier shell correlation=     0.8721
Average correlation coefficient      =     0.7434
Overall figure of merit              =     0.5547
-----------------------------------------------------------------------------
 Gamma decreased to    2.19674082E-03
  Iterations          173
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.28332713E-05  0.122252144       6.46210136E-03
   2917061.25       2928336.00      0.381966025      0.381966025     F
 fvalues    132216.844       12119.2490       2917061.25       2928336.00    


     CGMAT cycle number =        7

 Weight matrix    5.99999949E-02
 Actual weight    22.1333675      is applied to the X-ray term


 function value    2938628.75    

-------------------------------------------------------------------------------
             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 =     1.4593, B  =   -0.0972
Partial structure    1: scale =     0.3866, B  =   55.7022
Overall anisotropic scale factors
   B11 =   4.70 B22 =  -1.45 B33 =  -3.26 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3263
Average Fourier shell correlation    =     0.8805
AverageFree Fourier shell correlation=     0.8717
Average correlation coefficient      =     0.7436
Overall figure of merit              =     0.5531
-----------------------------------------------------------------------------
 Gamma decreased to    0.00000000    
  Iterations          353
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.87493765E-06  0.137069508       7.88528286E-03
   2938628.75       2917061.25      0.236067981      0.236067981     T
 fvalues    132222.656       12095.9082       2938628.75       2917061.25    


     CGMAT cycle number =        8

 Weight matrix    5.99999987E-02
 Actual weight    22.0640965      is applied to the X-ray term


 function value    2928636.75    

-------------------------------------------------------------------------------
             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 =     1.4606, B  =   -0.0460
Partial structure    1: scale =     0.3868, B  =   55.7586
Overall anisotropic scale factors
   B11 =   4.71 B22 =  -1.45 B33 =  -3.26 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2543
Free R factor                        =     0.3259
Average Fourier shell correlation    =     0.8806
AverageFree Fourier shell correlation=     0.8717
Average correlation coefficient      =     0.7438
Overall figure of merit              =     0.5540
-----------------------------------------------------------------------------
 iters          800   3.14950555E-08   7.62854724E-10  0.524245858       1.45514689E-09
 Not converging with gamma equal    0.00000000    
 Trying gamma equal    2.82878354E-02   0.00000000    
 Gamma decreased to    2.26302687E-02
  Iterations           95
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.25292163E-05   3.17606702E-02   1.63989002E-03
   2928636.75       2938628.75      0.236067981      0.236067981     F
 fvalues    132185.484       12083.4287       2928636.75       2938628.75    


     CGMAT cycle number =        9

 Weight matrix    5.99999949E-02
 Actual weight    22.0984802      is applied to the X-ray term


 function value    2933266.50    

-------------------------------------------------------------------------------
             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 =     1.4605, B  =   -0.0714
Partial structure    1: scale =     0.3867, B  =   55.7763
Overall anisotropic scale factors
   B11 =   4.71 B22 =  -1.44 B33 =  -3.26 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3258
Average Fourier shell correlation    =     0.8805
AverageFree Fourier shell correlation=     0.8716
Average correlation coefficient      =     0.7438
Overall figure of merit              =     0.5531
-----------------------------------------------------------------------------
 Gamma decreased to    1.74870268E-02
  Iterations          107
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.13934939E-05   3.16610746E-02   1.61022937E-03
   2933266.50       2928636.75      0.200000003      0.200000003     T
 fvalues    132189.484       12079.7207       2933266.50       2928636.75    


     CGMAT cycle number =       10

 Weight matrix    5.99999987E-02
 Actual weight    21.9561996      is applied to the X-ray term


 function value    2914421.00    

-------------------------------------------------------------------------------
             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 =     1.4605, B  =   -0.0871
Partial structure    1: scale =     0.3868, B  =   55.8421
Overall anisotropic scale factors
   B11 =   4.70 B22 =  -1.44 B33 =  -3.26 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2544
Free R factor                        =     0.3260
Average Fourier shell correlation    =     0.8811
AverageFree Fourier shell correlation=     0.8722
Average correlation coefficient      =     0.7438
Overall figure of merit              =     0.5550
-----------------------------------------------------------------------------
 Gamma decreased to    1.28113516E-02
  Iterations          122
  Convergence reached with no gamma cycles 
 average, maximum and rms of positional shifts   -1.06545494E-05   4.21096943E-02   1.95421255E-03
   2914421.00       2933266.50      0.200000003      0.200000003     F
 fvalues    132187.781       12079.8262       2914421.00       2933266.50    

 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_1-90A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   3054     2.012     1.652
Bond angles  : others                          5250     0.620     1.577
Torsion angles, period  1. refined              265     7.577     5.000
Torsion angles, period  2. refined               19    10.583     5.000
Torsion angles, period  3. refined              475    20.772    10.000
Torsion angles, period  6. refined              116    15.786    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                   577     0.254     0.200
VDW repulsions.others                          2177     0.206     0.200
VDW; torsion: refined_atoms                    1137     0.194     0.200
VDW; torsion.others                            1331     0.089     0.200
HBOND: refined_atoms                             58     0.208     0.200
HBOND.others                                      1     0.305     0.200
VDW repulsions: symmetry: refined_atoms           5     0.221     0.200
VDW repulsions: symmetry: others                 40     0.204     0.200
HBOND: symmetry: refined_atoms                    3     0.125     0.200
M. chain bond B values: refined atoms          1075     8.512     6.696
M. chain bond B values: others                 1075     8.503     6.694
M. chain angle B values: refined atoms         1335    10.782    11.963
M. chain angle B values: others                1336    10.781    11.970
S. chain bond B values: refined atoms          1209     9.996     7.564
S. chain bond B values: others                 1210     9.992     7.568
S. chain angle B values: refined atoms         1719    13.990    13.503
S. chain angle B values: others                1720    13.986    13.506
Long range B values: refined atoms             2693    15.806    63.271
Long range B values: others                    2692    15.813    63.287
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4604, B  =   -0.0639
Partial structure    1: scale =     0.3868, B  =   55.8281
Overall anisotropic scale factors
   B11 =   4.70 B22 =  -1.44 B33 =  -3.26 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   276.8   273.7  0.20  0.20     153   263.7   259.2  0.29  0.29
 0.083    5552  99.88   137.2   124.9  0.21  0.19     305   136.6   125.9  0.28  0.27
 0.139    7124  99.77    45.7    47.1  0.28  0.24     364    47.4    50.4  0.36  0.32
 0.194    8355  99.91    24.8    22.1  0.39  0.38     424    24.7    22.0  0.41  0.39
 0.249    8476  89.91    19.7    10.0  0.54  0.55     428    20.3    10.5  0.53  0.53
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.829    698   0.760   3240   0.814  0.936  0.9413  0.9739  0.8477  0.9293
  0.0834   4838   0.801    714   0.710   5552   0.789  1.001  0.9488  0.9737  0.8561  0.9321
  0.1387   6411   0.686    713   0.636   7124   0.681  0.802  0.9195  0.9504  0.7158  0.8723
  0.1940   7643   0.350    712   0.312   8355   0.347  0.457  0.7825  0.7967  0.6999  0.7079
  0.2493   7833   0.393    643   0.382   8476   0.392  0.812  0.8386  0.8072  0.4111  0.4769
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2544
Free R factor                        =     0.3261
Average Fourier shell correlation    =     0.8804
AverageFree Fourier shell correlation=     0.8714
Overall weighted R factor            =     0.2212
Free weighted R factor               =     0.2960
Overall weighted R2 factor           =     0.2296
Free weighted R2 factor              =     0.3175
Average correlation coefficient      =     0.7438
Overall correlation coefficient      =     0.9616
Free correlation coefficient         =     0.9201
Cruickshanks DPI for coordinate error=     0.1545
DPI based on free R factor           =     0.1681
Overall figure of merit              =     0.5526
ML based su of positional parameters =     0.2536
ML based su of thermal parameters    =    10.4030
-----------------------------------------------------------------------------
  Time in seconds: CPU =        11.01
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2537   0.3260   0.567      132409.    6910.4   0.0112  0.901   2.064  1.205   0.086
       1   0.2543   0.3245   0.555      132245.    6909.3   0.0104  0.844   2.008  1.171   0.083
       2   0.2543   0.3258   0.553      132218.    6910.5   0.0107  0.863   2.015  1.177   0.083
       3   0.2543   0.3260   0.555      132180.    6908.8   0.0106  0.861   2.014  1.176   0.083
       4   0.2544   0.3260   0.554      132203.    6910.0   0.0106  0.859   2.012  1.175   0.083
       5   0.2544   0.3262   0.555      132217.    6910.9   0.0106  0.860   2.012  1.175   0.083
       6   0.2544   0.3263   0.553      132223.    6911.5   0.0106  0.859   2.012  1.174   0.083
       7   0.2543   0.3259   0.554      132185.    6909.2   0.0106  0.860   2.012  1.175   0.083
       8   0.2544   0.3258   0.553      132189.    6909.6   0.0106  0.860   2.012  1.175   0.083
       9   0.2544   0.3260   0.555      132188.    6909.7   0.0106  0.860   2.013  1.175   0.083
      10   0.2544   0.3261   0.553      132194.    6910.0   0.0106  0.860   2.012  1.175   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2537   0.2544
             R free    0.3260   0.3261
     Rms BondLength    0.0112   0.0106
      Rms BondAngle    2.0637   2.0125
     Rms ChirVolume    0.0857   0.0828
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0403   
Times: User:      15.3s System:    0.1s Elapsed:     0:15