# Date 2008-01-16 Time 05:34:46 PST -0800 (1200490486.26 s)
#phil __OFF__

Command line arguments: "../791.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25433
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 791

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.93, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.00219
Completeness in resolution range: 0.960057
Completeness with d_max=infinity: 0.957102

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   2.0022

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.00219
Completeness in resolution range: 0.960057
Completeness with d_max=infinity: 0.957102

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.2841 [2148/2172]  1929   219  10.2%
  bin  2:  4.2841 -  3.4132 [2053/2073]  1849   204   9.9%
  bin  3:  3.4132 -  2.9855 [2030/2049]  1832   198   9.8%
  bin  4:  2.9855 -  2.7143 [2013/2043]  1810   203  10.1%
  bin  5:  2.7143 -  2.5207 [1997/2016]  1796   201  10.1%
  bin  6:  2.5207 -  2.3726 [2007/2032]  1802   205  10.2%
  bin  7:  2.3726 -  2.2542 [1971/1999]  1776   195   9.9%
  bin  8:  2.2542 -  2.1564 [1968/2004]  1772   196  10.0%
  bin  9:  2.1564 -  2.0736 [1957/1999]  1765   192   9.8%
  bin 10:  2.0736 -  2.0022 [1445/2017]  1299   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 9
        2.22 -     2.89: 1310
        2.89 -     3.56: 4371
        3.56 -     4.23: 9054
        4.23 -     4.90: 13144
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.553 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.720 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.720 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.767 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27883 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_001.geo

CPU time processing inputs: 9.02


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.93 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3641   r_free= 0.3553   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.150827                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7782 0.99   1392  154 0.3108 0.2900      6.4395      6.3302|
|  2:  4.7782 -  3.8125 0.99   1339  152 0.2882 0.3034      6.5916      6.6749|
|  3:  3.8125 -  3.3365 0.99   1303  142 0.3304 0.2853      6.5182      6.4139|
|  4:  3.3365 -  3.0341 0.99   1310  145 0.3385 0.3499      6.3601       6.355|
|  5:  3.0341 -  2.8181 0.99   1296  147 0.3790 0.3349      6.2406      6.2083|
|  6:  2.8181 -  2.6529 0.99   1298  143 0.3716 0.4153      6.1235       6.115|
|  7:  2.6529 -  2.5207 0.99   1278  142 0.3931 0.3832      6.1125      6.0553|
|  8:  2.5207 -  2.4114 0.98   1279  138 0.4046 0.3773      6.0883      6.0825|
|  9:  2.4114 -  2.3189 0.98   1274  145 0.3911 0.4107      5.9997       6.031|
| 10:  2.3189 -  2.2391 1.00   1296  141 0.4291 0.3774      6.0356      5.9611|
| 11:  2.2391 -  2.1693 0.97   1257  140 0.4263 0.4207      5.9545       5.983|
| 12:  2.1693 -  2.1075 0.98   1252  144 0.4211 0.3905      5.8908      5.9221|
| 13:  2.1075 -  2.0521 0.99   1276  135 0.4139 0.4580      5.7859       5.795|
| 14:  2.0521 -  2.0022 0.60    780   91 0.3776 0.3613      5.7446      5.6486|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7782  1392   154  0.79  26.06   0.84     0.81      43732.47|
|  2:  4.7782 -  3.8125  1339   152  0.82  24.39   0.94     0.89      58044.10|
|  3:  3.8125 -  3.3365  1303   142  0.76  29.71   0.94     0.89      58581.40|
|  4:  3.3365 -  3.0341  1310   145  0.71  34.36   0.95     0.84      52904.08|
|  5:  3.0341 -  2.8181  1296   147  0.65  39.72   0.96     0.79      43183.47|
|  6:  2.8181 -  2.6529  1298   143  0.62  42.53   0.95     0.76      41002.23|
|  7:  2.6529 -  2.5207  1278   142  0.61  43.19   0.97     0.77      37283.68|
|  8:  2.5207 -  2.4114  1279   138  0.62  42.55   0.95     0.79      33703.95|
|  9:  2.4114 -  2.3189  1274   145  0.63  42.07   0.99     0.81      30893.88|
| 10:  2.3189 -  2.2391  1296   141  0.60  44.01   1.00     0.80      28564.70|
| 11:  2.2391 -  2.1693  1257   140  0.59  44.69   0.97     0.82      28797.28|
| 12:  2.1693 -  2.1075  1252   144  0.59  44.86   0.99     0.81      25976.79|
| 13:  2.1075 -  2.0521  1276   135  0.57  47.04   0.97     0.80      23426.49|
| 14:  2.0521 -  2.0022   780    91  0.59  45.15   1.03     0.76      20066.61|
|alpha:            min =        0.76 max =            0.89 mean =         0.81|
|beta:             min =    20066.61 max =        58581.40 mean =     38276.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.99 mean =        38.98|
|phase err.(test): min =        0.00 max =           89.62 mean =        38.60|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.752874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.026   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.890683              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.253   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.553 -  1.888:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.888 -  2.222:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.222 -  2.557:       20 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.557 -  2.892:     1290 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.892 -  3.226:     1867 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.226 -  3.561:     2504 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.561 -  3.896:     4607 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.896 -  4.231:     4447 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.231 -  4.565:     5978 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.565 -  4.900:     7166 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.553 |       0.226 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3641   r_free= 0.3553   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.150827                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3446   r_free= 0.3405   ksol= 0.31   Bsol= 56.57   scale= 0.961   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-3.22,6.28,-0.00,0.00,0.00); trace/3= 0.04                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.123793                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.079389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.746   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.489935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.936   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3446      final r-factor (work) = 0.2350          |
| start r-factor (free) = 0.3405      final r-factor (free) = 0.2631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7151 = 5.08 * 0.50 * 6.1218 + 1.00 * 0.1677                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0522 = 5.08 * 0.50 * 5.8894 + 1.00 * 0.0949                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2350      final r-factor (work) = 0.2157          |
| start r-factor (free) = 0.2631      final r-factor (free) = 0.2677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8918 = 0.49 * 1.00 * 5.8894 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8600 = 0.49 * 1.00 * 5.7050 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.25  16.97    None  None   None       |
|    all(noH): 2823   0      0.00    114.25  16.97    None  None   None       |
|    Sol.    : 438    0      3.40    64.33   38.09    None  None   None       |
|    Mac.    : 2385   0      0.00    114.25  13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.425: 1176   |   5:    57.125 -  68.550:   23        |
|      1:    11.425 -  22.850: 1059   |   6:    68.550 -  79.975:    0        |
|      2:    22.850 -  34.275:  257   |   7:    79.975 -  91.400:    0        |
|      3:    34.275 -  45.700:  180   |   8:    91.400 - 102.825:    0        |
|      4:    45.700 -  57.125:  127   |   9:   102.825 - 114.250:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2157 r_free = 0.2677             target_work(ml) = 5.711         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2153 r_free = 0.2677             target_work(ml) = 5.710         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2153   r_free= 0.2677   ksol= 0.31   Bsol= 56.57   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-3.22,6.28,-0.00,0.00,0.00); trace/3= 0.04                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.710200                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2114   r_free= 0.2643   ksol= 0.34   Bsol= 71.97   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.59,1.59,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.698186                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.164842              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.317   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.529916              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.727   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2114      final r-factor (work) = 0.1516          |
| start r-factor (free) = 0.2643      final r-factor (free) = 0.1961          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9690 = 4.16 * 0.50 * 5.7021 + 1.00 * 0.0949                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6483 = 4.16 * 0.50 * 5.5584 + 1.00 * 0.0735                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1516      final r-factor (work) = 0.1376          |
| start r-factor (free) = 0.1961      final r-factor (free) = 0.1838          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0037 = 0.53 * 1.00 * 5.5584 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8425 = 0.53 * 1.00 * 5.3434 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.25   17.63    None  None   None       |
|    all(noH): 2823   0      0.00    83.25   17.63    None  None   None       |
|    Sol.    : 438    0      4.95    83.25   42.26    None  None   None       |
|    Mac.    : 2385   0      0.00    76.74   13.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.325:  658   |   5:    41.627 -  49.953:   81        |
|      1:     8.325 -  16.651: 1316   |   6:    49.953 -  58.278:  103        |
|      2:    16.651 -  24.976:  334   |   7:    58.278 -  66.603:   60        |
|      3:    24.976 -  33.302:  128   |   8:    66.603 -  74.929:   28        |
|      4:    33.302 -  41.627:  105   |   9:    74.929 -  83.254:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1376 r_free = 0.1838             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1374 r_free = 0.1836             target_work(ml) = 5.311         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1374   r_free= 0.1836   ksol= 0.34   Bsol= 71.97   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.59,1.59,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.311169                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1822   ksol= 0.34   Bsol= 76.88   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.40,0.19,-0.00,0.00,0.00); trace/3= -1.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305386                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.174729              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.679  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.273469              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.974  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1368      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1822      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5540 = 3.17 * 0.50 * 5.3423 + 1.00 * 0.0738                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4141 = 3.17 * 0.50 * 5.2547 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4477 = 0.27 * 1.00 * 5.2547 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4311 = 0.27 * 1.00 * 5.1997 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    83.54   17.05    None  None   None       |
|    all(noH): 2823   0      1.01    83.54   17.05    None  None   None       |
|    Sol.    : 438    0      3.44    83.54   40.34    None  None   None       |
|    Mac.    : 2385   0      1.01    78.64   12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.008 -   9.261:  886   |   5:    42.275 -  50.528:   87        |
|      1:     9.261 -  17.515: 1182   |   6:    50.528 -  58.782:   76        |
|      2:    17.515 -  25.768:  270   |   7:    58.782 -  67.035:   45        |
|      3:    25.768 -  34.022:  131   |   8:    67.035 -  75.289:   21        |
|      4:    34.022 -  42.275:  118   |   9:    75.289 -  83.542:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1640             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1638             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1638   ksol= 0.34   Bsol= 76.88   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.40,0.19,-0.00,0.00,0.00); trace/3= -1.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.187842                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1637   ksol= 0.33   Bsol= 65.71   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.19,-0.08,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.187188                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.109830              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.165  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.138624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.226  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1570 = 3.11 * 0.50 * 5.1990 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1170 = 3.11 * 0.50 * 5.1701 + 1.00 * 0.0780                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7258 = 0.14 * 1.00 * 5.1701 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7239 = 0.14 * 1.00 * 5.1687 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    80.54   16.44    None  None   None       |
|    all(noH): 2823   0      1.35    80.54   16.44    None  None   None       |
|    Sol.    : 438    0      1.35    80.54   37.69    None  None   None       |
|    Mac.    : 2385   0      1.71    75.10   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.345 -   9.265:  883   |   5:    40.945 -  48.865:   87        |
|      1:     9.265 -  17.185: 1188   |   6:    48.865 -  56.784:   76        |
|      2:    17.185 -  25.105:  278   |   7:    56.784 -  64.704:   33        |
|      3:    25.105 -  33.025:  133   |   8:    64.704 -  72.624:   15        |
|      4:    33.025 -  40.945:  124   |   9:    72.624 -  80.544:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1610             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1608             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1608   ksol= 0.33   Bsol= 65.71   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.19,-0.08,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.165615                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1597   ksol= 0.33   Bsol= 65.71   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.24,-0.27,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161965                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.716747              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.550  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.892991              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.437  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5135 = 1.72 * 0.50 * 5.1674 + 1.00 * 0.0780                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5010 = 1.72 * 0.50 * 5.1723 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6262 = 0.89 * 1.00 * 5.1723 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6259 = 0.89 * 1.00 * 5.1692 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.30    90.18   16.83    None  None   None       |
|    all(noH): 2823   0      0.30    90.18   16.83    None  None   None       |
|    Sol.    : 438    0      0.44    90.18   39.96    None  None   None       |
|    Mac.    : 2385   0      0.30    85.47   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.300 -   9.288:  961   |   5:    45.240 -  54.227:   97        |
|      1:     9.288 -  18.276: 1162   |   6:    54.227 -  63.215:   71        |
|      2:    18.276 -  27.264:  246   |   7:    63.215 -  72.203:   35        |
|      3:    27.264 -  36.252:  132   |   8:    72.203 -  81.191:    9        |
|      4:    36.252 -  45.240:  106   |   9:    81.191 -  90.179:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1622             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1622             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1622   ksol= 0.33   Bsol= 65.71   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.24,-0.27,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174837                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7782 0.99   1392  154 0.1005 0.1291      5.3985       5.541|
|  2:  4.7782 -  3.8125 0.99   1339  152 0.0875 0.1139      5.4499      5.6551|
|  3:  3.8125 -  3.3365 0.99   1303  142 0.1076 0.1471      5.4919      5.8186|
|  4:  3.3365 -  3.0341 0.99   1310  145 0.1239 0.1711      5.4679      5.6314|
|  5:  3.0341 -  2.8181 0.99   1296  147 0.1375 0.1659      5.3571      5.5654|
|  6:  2.8181 -  2.6529 0.99   1298  143 0.1271 0.2106      5.2517      5.5607|
|  7:  2.6529 -  2.5207 0.99   1278  142 0.1346 0.1670      5.2167      5.3495|
|  8:  2.5207 -  2.4114 0.98   1279  138 0.1198 0.1712       5.112      5.3804|
|  9:  2.4114 -  2.3189 0.98   1274  145 0.1197 0.1916      5.0716      5.3517|
| 10:  2.3189 -  2.2391 1.00   1296  141 0.1178 0.1746      4.9845      5.2083|
| 11:  2.2391 -  2.1693 0.97   1257  140 0.1176 0.1775      4.9724      5.2529|
| 12:  2.1693 -  2.1075 0.98   1252  144 0.1179 0.1825      4.9225      5.2897|
| 13:  2.1075 -  2.0521 0.99   1276  135 0.1131 0.1727      4.8211      5.0437|
| 14:  2.0521 -  2.0022 0.60    780   91 0.0966 0.1766        4.68      4.9607|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7782  1392   154  0.94   9.17   0.96     0.93       7173.90|
|  2:  4.7782 -  3.8125  1339   152  0.95   7.94   1.00     0.99       9130.10|
|  3:  3.8125 -  3.3365  1303   142  0.93  11.28   1.01     1.01      10461.23|
|  4:  3.3365 -  3.0341  1310   145  0.92  13.78   0.99     0.97      10406.18|
|  5:  3.0341 -  2.8181  1296   147  0.90  16.05   0.99     0.97       8739.61|
|  6:  2.8181 -  2.6529  1298   143  0.89  16.89   0.97     0.94       7660.22|
|  7:  2.6529 -  2.5207  1278   142  0.90  16.42   0.98     0.94       6791.10|
|  8:  2.5207 -  2.4114  1279   138  0.90  15.84   0.98     0.95       5816.44|
|  9:  2.4114 -  2.3189  1274   145  0.91  15.59   0.99     0.95       5405.17|
| 10:  2.3189 -  2.2391  1296   141  0.89  16.55   0.98     0.95       4660.93|
| 11:  2.2391 -  2.1693  1257   140  0.90  16.58   0.97     0.92       4611.86|
| 12:  2.1693 -  2.1075  1252   144  0.90  16.55   0.99     0.97       4349.82|
| 13:  2.1075 -  2.0521  1276   135  0.89  17.06   0.97     0.94       3697.98|
| 14:  2.0521 -  2.0022   780    91  0.92  14.31   0.95     0.91       2724.46|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     2724.46 max =        10461.23 mean =      6686.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.52|
|phase err.(test): min =        0.00 max =           89.84 mean =        13.96|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1620   ksol= 0.33   Bsol= 65.71   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.01,-0.11,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174952                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1620   ksol= 0.33   Bsol= 65.71   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.01,-0.11,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174952                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7782 0.99   1392  154 0.1005 0.1292      5.3992      5.5423|
|  2:  4.7782 -  3.8125 0.99   1339  152 0.0875 0.1140      5.4503      5.6551|
|  3:  3.8125 -  3.3365 0.99   1303  142 0.1076 0.1472      5.4919      5.8191|
|  4:  3.3365 -  3.0341 0.99   1310  145 0.1239 0.1711       5.468      5.6315|
|  5:  3.0341 -  2.8181 0.99   1296  147 0.1375 0.1658       5.357       5.565|
|  6:  2.8181 -  2.6529 0.99   1298  143 0.1271 0.2108      5.2518      5.5611|
|  7:  2.6529 -  2.5207 0.99   1278  142 0.1346 0.1670      5.2168      5.3495|
|  8:  2.5207 -  2.4114 0.98   1279  138 0.1198 0.1711      5.1122      5.3803|
|  9:  2.4114 -  2.3189 0.98   1274  145 0.1197 0.1917      5.0716      5.3518|
| 10:  2.3189 -  2.2391 1.00   1296  141 0.1178 0.1745      4.9845      5.2077|
| 11:  2.2391 -  2.1693 0.97   1257  140 0.1176 0.1774      4.9722      5.2522|
| 12:  2.1693 -  2.1075 0.98   1252  144 0.1179 0.1823      4.9222      5.2892|
| 13:  2.1075 -  2.0521 0.99   1276  135 0.1131 0.1730      4.8213      5.0446|
| 14:  2.0521 -  2.0022 0.60    780   91 0.0966 0.1766      4.6806      4.9605|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7782  1392   154  0.94   9.18   0.96     0.94       7188.70|
|  2:  4.7782 -  3.8125  1339   152  0.95   7.95   1.00     0.99       9140.61|
|  3:  3.8125 -  3.3365  1303   142  0.93  11.28   1.02     1.01      10462.80|
|  4:  3.3365 -  3.0341  1310   145  0.92  13.79   1.00     0.98      10406.50|
|  5:  3.0341 -  2.8181  1296   147  0.90  16.05   1.00     0.97       8741.71|
|  6:  2.8181 -  2.6529  1298   143  0.89  16.89   0.98     0.95       7659.62|
|  7:  2.6529 -  2.5207  1278   142  0.90  16.42   0.98     0.95       6792.80|
|  8:  2.5207 -  2.4114  1279   138  0.90  15.85   0.99     0.96       5818.13|
|  9:  2.4114 -  2.3189  1274   145  0.91  15.59   1.00     0.96       5406.97|
| 10:  2.3189 -  2.2391  1296   141  0.89  16.55   0.99     0.95       4657.11|
| 11:  2.2391 -  2.1693  1257   140  0.90  16.57   0.98     0.93       4607.01|
| 12:  2.1693 -  2.1075  1252   144  0.90  16.55   1.00     0.98       4346.06|
| 13:  2.1075 -  2.0521  1276   135  0.89  17.06   0.98     0.95       3698.76|
| 14:  2.0521 -  2.0022   780    91  0.92  14.32   0.96     0.92       2727.59|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2727.59 max =        10462.80 mean =      6687.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.52|
|phase err.(test): min =        0.00 max =           89.84 mean =        13.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.29    90.17   16.83    None  None   None       |
|    all(noH): 2823   0      0.29    90.17   16.83    None  None   None       |
|    Sol.    : 438    0      0.43    90.17   39.95    None  None   None       |
|    Mac.    : 2385   0      0.29    85.46   12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.292 -   9.280:  961   |   5:    45.231 -  54.219:   97        |
|      1:     9.280 -  18.268: 1162   |   6:    54.219 -  63.207:   71        |
|      2:    18.268 -  27.256:  246   |   7:    63.207 -  72.195:   35        |
|      3:    27.256 -  36.243:  132   |   8:    72.195 -  81.183:    9        |
|      4:    36.243 -  45.231:  106   |   9:    81.183 -  90.171:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 284         
Filter by distance & map next to the model:
   mapped sites are within: 0.537 - 4.822
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 279 from: 284
   mapped sites are within: 0.706 - 4.822

peak=    5.379 closest distance to " CB  GLN A 223 " =    1.457
peak=    5.233 closest distance to " O   HOH Z 113 " =    2.187
peak=    5.178 closest distance to " CZ  PHE A 218 " =    1.104
peak=    5.094 closest distance to " CG  PRO A  54 " =    1.405
peak=    4.887 closest distance to " CB  PRO A  54 " =    1.008
peak=    4.837 closest distance to " NE2 GLN A  11 " =    1.093
peak=    4.779 closest distance to " CG  PRO A 198 " =    1.307
peak=    4.752 closest distance to " CB  ARG A 190 " =    1.592
peak=    4.746 closest distance to " O   HOH Z 298 " =    2.024
peak=    4.737 closest distance to " O   HOH Z 142 " =    1.793
peak=    4.650 closest distance to " CB  GLN A 183 " =    1.246
peak=    4.623 closest distance to " O   HOH Z 189 " =    2.939
peak=    4.598 closest distance to " O   HOH Z 126 " =    1.911
peak=    4.588 closest distance to " O   HOH Z 369 " =    2.184
peak=    4.535 closest distance to " O   HOH Z 232 " =    2.309
peak=    4.511 closest distance to " CG  PRO A 213 " =    1.193
peak=    4.436 closest distance to " CB  ARG A 275 " =    0.914
peak=    4.420 closest distance to " CA  TYR A  30 " =    0.989
peak=    4.411 closest distance to " CB  ARG A  79 " =    1.383
peak=    4.382 closest distance to " CG2 VAL A 257 " =    0.852
peak=    4.361 closest distance to " CB  ASN A 148 " =    1.477
peak=    4.326 closest distance to " CB  SER A  63 " =    1.184
peak=    4.314 closest distance to " CE  LYS A  76 " =    0.903
peak=    4.313 closest distance to " O  BHOH Z  74 " =    1.228
peak=    4.280 closest distance to " O   HOH Z  53 " =    2.502
peak=    4.206 closest distance to " CB  LEU A 228 " =    1.101
peak=    4.203 closest distance to " ND2 ASN A 187 " =    1.455
peak=    4.191 closest distance to " CZ3 TRP A 266 " =    1.111
peak=    4.136 closest distance to " CB  VAL A 265 " =    1.240
peak=    4.135 closest distance to " CG  PRO A 243 " =    1.058
peak=    4.128 closest distance to " O   HOH Z 406 " =    1.718
peak=    4.109 closest distance to " CD  ARG A 159 " =    0.761
peak=    4.097 closest distance to " CB  TRP A 266 " =    1.057
peak=    4.089 closest distance to " CB  ASN A 142 " =    1.015
peak=    4.082 closest distance to " O   HOH Z 214 " =    2.324
peak=    4.077 closest distance to " CB  GLU A 277 " =    3.755
peak=    4.068 closest distance to " CB  TYR A 169 " =    0.721
peak=    4.052 closest distance to " CA  ALA A  51 " =    0.941
peak=    4.035 closest distance to " O   HOH Z   9 " =    2.129
peak=    4.027 closest distance to " CE1 PHE A  38 " =    1.223
peak=    4.016 closest distance to " NH1AARG A 145 " =    1.331
peak=    4.009 closest distance to " CB  ASP A 124 " =    0.797
peak=    3.987 closest distance to " CA  ARG A 195 " =    1.259
peak=    3.986 closest distance to " ND2 ASN A 249 " =    0.878
peak=    3.969 closest distance to " CD  LYS A 166 " =    1.268
peak=    3.957 closest distance to " O   THR A 220 " =    1.218
peak=    3.938 closest distance to " O   HOH Z 313 " =    2.012
peak=    3.931 closest distance to " C   PRO A 198 " =    1.513
peak=    3.930 closest distance to " CB  VAL A 202 " =    1.537
peak=    3.926 closest distance to " O   HOH Z 287 " =    1.996
peak=    3.924 closest distance to " CA  ASN A 215 " =    1.100
peak=    3.919 closest distance to " CB  ASN A  39 " =    0.908
peak=    3.916 closest distance to " O   HOH Z  78 " =    1.644
peak=    3.909 closest distance to " CB  SER A 210 " =    0.822
peak=    3.905 closest distance to " CB  PRO A  90 " =    1.142
peak=    3.901 closest distance to " CG  MET A 185 " =    1.160
peak=    3.900 closest distance to " O   HOH Z 368 " =    2.167
peak=    3.897 closest distance to " O   HOH Z 265 " =    2.153
peak=    3.894 closest distance to " CB  LEU A  83 " =    0.753
peak=    3.887 closest distance to " CD2 TRP A 179 " =    1.301
peak=    3.884 closest distance to " O   HOH Z 427 " =    3.056
peak=    3.881 closest distance to " CB  GLU A 128 " =    0.895
peak=    3.875 closest distance to " O   HOH Z  43 " =    1.956
peak=    3.867 closest distance to " O  BHOH Z 338 " =    2.328
peak=    3.860 closest distance to " O   HOH Z  63 " =    2.001
peak=    3.859 closest distance to " CA  THR A 264 " =    0.935
peak=    3.855 closest distance to " O   ASN A  74 " =    1.352
peak=    3.847 closest distance to " CB  GLU A  46 " =    0.997
peak=    3.842 closest distance to " O   HOH Z 158 " =    3.176
peak=    3.830 closest distance to " O   SER A  87 " =    2.342
peak=    3.829 closest distance to " O   HOH Z 303 " =    2.162
peak=    3.820 closest distance to " CB  ASP A 140 " =    1.083
peak=    3.802 closest distance to " O   HOH Z 133 " =    2.752
peak=    3.800 closest distance to " OE1 GLN A  55 " =    1.524
peak=    3.798 closest distance to " CG  LEU A 167 " =    1.254
peak=    3.795 closest distance to " CB  ALA A 104 " =    0.710
peak=    3.793 closest distance to " NZ  LYS A 117 " =    3.192
peak=    3.789 closest distance to " CB  ASN A 110 " =    1.117
peak=    3.787 closest distance to " CA  SER A  87 " =    1.020
peak=    3.782 closest distance to " CD  ARG A 269 " =    0.945
peak=    3.774 closest distance to " O   HOH Z 180 " =    2.208
peak=    3.765 closest distance to " CD1 LEU A  96 " =    0.765
peak=    3.732 closest distance to " O   HOH Z 234 " =    3.847
peak=    3.731 closest distance to " O   HOH Z 316 " =    3.150
peak=    3.729 closest distance to " CD1 LEU A 300 " =    1.136
peak=    3.718 closest distance to " O   HOH Z 346 " =    1.737
peak=    3.714 closest distance to " O   HOH Z 353 " =    2.614
peak=    3.713 closest distance to " O   HOH Z  21 " =    1.790
peak=    3.712 closest distance to " CB  GLU A 152 " =    1.257
peak=    3.706 closest distance to " CB  ASN A 187 " =    1.255
peak=    3.700 closest distance to " O   HOH Z 172 " =    3.371
peak=    3.684 closest distance to " O   HOH Z  10 " =    1.809
peak=    3.677 closest distance to " CA  ARG A  36 " =    1.086
peak=    3.677 closest distance to " O   HOH Z 411 " =    4.078
peak=    3.668 closest distance to " CG2 ILE A 120 " =    1.162
peak=    3.662 closest distance to " O   HOH Z 294 " =    1.607
peak=    3.658 closest distance to " NE2 HIS A 207 " =    1.135
peak=    3.635 closest distance to " CA  ALA A 160 " =    1.017
peak=    3.625 closest distance to " N   ASN A  39 " =    1.262
peak=    3.619 closest distance to " CB  LYS A 117 " =    1.218
peak=    3.613 closest distance to " O   HOH Z 359 " =    1.580
peak=    3.608 closest distance to " CB  MET A  40 " =    0.799
peak=    3.601 closest distance to " CD  ARG A  66 " =    2.376
peak=    3.590 closest distance to " O   HOH Z 423 " =    1.892
peak=    3.579 closest distance to " O   HOH Z  40 " =    1.942
peak=    3.571 closest distance to " CB  ILE A 120 " =    1.246
peak=    3.566 closest distance to " O   HOH Z 203 " =    1.747
peak=    3.560 closest distance to " CG1 VAL A 153 " =    0.996
peak=    3.557 closest distance to " O   HOH Z 248 " =    1.585
peak=    3.556 closest distance to " CB  ALA A 291 " =    1.077
peak=    3.553 closest distance to " O   HOH Z 285 " =    2.154
peak=    3.541 closest distance to " CA  ALA A 154 " =    1.074
peak=    3.539 closest distance to " O   HOH Z  68 " =    2.188
peak=    3.537 closest distance to " O   HOH Z 394 " =    4.026
peak=    3.536 closest distance to " ND2 ASN A 249 " =    1.875
peak=    3.528 closest distance to " O   HOH Z 250 " =    1.432
peak=    3.526 closest distance to " O   HOH Z 280 " =    3.005
peak=    3.523 closest distance to " O   HOH Z 392 " =    2.871
peak=    3.517 closest distance to " CA  TYR A 116 " =    1.382
peak=    3.516 closest distance to " CG2AVAL A  72 " =    1.717
peak=    3.513 closest distance to " CA  ILE A 234 " =    0.997
peak=    3.513 closest distance to " O   HOH Z 183 " =    1.410
peak=    3.512 closest distance to " OG BSER A 134 " =    2.858
peak=    3.506 closest distance to " O   HOH Z 148 " =    3.514
peak=    3.500 closest distance to " OD1 ASN A  69 " =    2.599
peak=    3.499 closest distance to " CA  VAL A 125 " =    1.140
peak=    3.498 closest distance to " OG BSER A 164 " =    2.317
peak=    3.496 closest distance to " O   ALA A 165 " =    1.631
peak=    3.493 closest distance to " O   HOH Z 261 " =    1.864
peak=    3.484 closest distance to " CA  GLN A  94 " =    0.767
peak=    3.483 closest distance to " CB  ALA A 114 " =    0.832
peak=    3.483 closest distance to " O   HOH Z 193 " =    1.791
peak=    3.481 closest distance to " O   THR A 182 " =    1.393
peak=    3.479 closest distance to " CB  SER A   3 " =    1.336
peak=    3.479 closest distance to " O   HOH Z 419 " =    2.155
peak=    3.473 closest distance to " O   HOH Z 368 " =    3.561
peak=    3.466 closest distance to " O   THR A 251 " =    1.107
peak=    3.462 closest distance to " O   HOH Z  61 " =    1.666
peak=    3.457 closest distance to " O   HOH Z 337 " =    3.617
peak=    3.453 closest distance to " CB  SER A 212 " =    1.273
peak=    3.453 closest distance to " CA  ARG A 139 " =    0.984
peak=    3.449 closest distance to " CG  GLU A  37 " =    0.909
peak=    3.447 closest distance to " N   ARG A 156 " =    1.361
peak=    3.444 closest distance to " O   ASN A  74 " =    2.093
peak=    3.433 closest distance to " CB  ASN A 215 " =    1.148
peak=    3.433 closest distance to " O   HOH Z 365 " =    2.890
peak=    3.432 closest distance to " O   HOH Z 383 " =    2.137
peak=    3.420 closest distance to " N   TYR A 116 " =    1.460
peak=    3.409 closest distance to " O   HOH Z 251 " =    1.647
peak=    3.409 closest distance to " CB  TYR A 116 " =    0.783
peak=    3.397 closest distance to " CG2 ILE A 239 " =    0.738
peak=    3.397 closest distance to " O   HOH Z 128 " =    2.261
peak=    3.396 closest distance to " CB  THR A  31 " =    1.609
peak=    3.394 closest distance to " CD BLYS A 290 " =    0.967
peak=    3.389 closest distance to " CB  MET A  47 " =    0.991
peak=    3.384 closest distance to " N   PHE A 130 " =    1.206
peak=    3.384 closest distance to " CB  PHE A 204 " =    0.752
peak=    3.379 closest distance to " O   HOH Z 272 " =    1.821
peak=    3.377 closest distance to " CA  MET A 105 " =    1.037
peak=    3.375 closest distance to " O   HOH Z 209 " =    2.283
peak=    3.373 closest distance to " CA  ASN A 217 " =    1.276
peak=    3.371 closest distance to " CD2 LEU A 297 " =    0.872
peak=    3.361 closest distance to " CA  ASP A 162 " =    1.017
peak=    3.359 closest distance to " CA  ASN A 127 " =    1.173
peak=    3.357 closest distance to " CH2 TRP A  70 " =    0.875
peak=    3.356 closest distance to " CB  SER A 141 " =    1.018
peak=    3.354 closest distance to " CG  GLN A  11 " =    1.671
peak=    3.335 closest distance to " CD1 ILE A 199 " =    0.910
peak=    3.334 closest distance to " O   HOH Z 166 " =    4.004
peak=    3.323 closest distance to " O   SER A 164 " =    1.556
peak=    3.322 closest distance to " O   HOH Z 185 " =    1.842
peak=    3.320 closest distance to " O   HOH Z 417 " =    3.380
peak=    3.315 closest distance to " O   HOH Z 426 " =    1.911
peak=    3.314 closest distance to " O   HOH Z 291 " =    1.550
peak=    3.311 closest distance to " CG AARG A 275 " =    1.171
peak=    3.307 closest distance to " CA  THR A 221 " =    1.077
peak=    3.306 closest distance to " O   PHE A 192 " =    1.398
peak=    3.305 closest distance to " CE1 TYR A 186 " =    1.391
peak=    3.299 closest distance to " O   HOH Z 213 " =    2.013
peak=    3.293 closest distance to " CB  GLN A  88 " =    1.212
peak=    3.290 closest distance to " O   HOH Z  88 " =    1.887
peak=    3.288 closest distance to " CG2 THR A 221 " =    1.088
peak=    3.280 closest distance to " O   HOH Z 116 " =    3.207
peak=    3.279 closest distance to " O   HOH Z 290 " =    0.984
peak=    3.273 closest distance to " O   PRO A 213 " =    1.460
peak=    3.270 closest distance to " CG2 ILE A 234 " =    0.806
peak=    3.269 closest distance to " O   HOH Z 193 " =    2.031
peak=    3.268 closest distance to " O   HOH Z 380 " =    1.941
peak=    3.265 closest distance to " NE  ARG A  79 " =    1.056
peak=    3.265 closest distance to " O   HOH Z 171 " =    4.054
peak=    3.265 closest distance to " CB  ARG A 138 " =    0.984
peak=    3.265 closest distance to " CA  ALA A 158 " =    1.319
peak=    3.264 closest distance to " O   HOH Z 421 " =    2.164
peak=    3.264 closest distance to " O   HOH Z 152 " =    2.185
peak=    3.257 closest distance to " O   PHE A  61 " =    1.387
peak=    3.257 closest distance to " CA  ALA A 233 " =    1.480
peak=    3.256 closest distance to " O   HOH Z 340 " =    2.124
peak=    3.253 closest distance to " CB  SER A 273 " =    0.907
peak=    3.252 closest distance to " CB  LEU A  96 " =    1.367
peak=    3.250 closest distance to " O   HOH Z 147 " =    1.914
peak=    3.247 closest distance to " OD1 ASP A 171 " =    1.282
peak=    3.247 closest distance to " CA  GLU A  46 " =    0.837
peak=    3.245 closest distance to " CG2 VAL A 197 " =    1.080
peak=    3.241 closest distance to " CA  ALA A 100 " =    0.942
peak=    3.241 closest distance to " O   HOH Z 218 " =    4.692
peak=    3.240 closest distance to " CA  ALA A 129 " =    1.268
peak=    3.235 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.233 closest distance to " O   HOH Z 371 " =    2.963
peak=    3.226 closest distance to " O   HOH Z  48 " =    1.596
peak=    3.225 closest distance to " O   HOH Z 325 " =    2.432
peak=    3.224 closest distance to " CD  ARG A 219 " =    1.121
peak=    3.223 closest distance to " CG2AVAL A 121 " =    2.385
peak=    3.219 closest distance to " CA  LEU A  83 " =    1.210
peak=    3.216 closest distance to " O   HOH Z  44 " =    2.969
peak=    3.215 closest distance to " O   HOH Z  90 " =    2.205
peak=    3.213 closest distance to " N   ASN A 127 " =    1.266
peak=    3.213 closest distance to " O   TYR A 116 " =    1.316
peak=    3.212 closest distance to " O   HOH Z  88 " =    2.804
peak=    3.210 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.206 closest distance to " OG1 THR A 264 " =    0.706
peak=    3.204 closest distance to " ND1 HIS A  86 " =    1.729
peak=    3.202 closest distance to " CB  GLU A  37 " =    0.958
peak=    3.198 closest distance to " CB  GLN A 205 " =    1.094
peak=    3.196 closest distance to " O   HOH Z   1 " =    2.203
peak=    3.195 closest distance to " O   HOH Z 305 " =    3.748
peak=    3.195 closest distance to " O   HOH Z  94 " =    2.386
peak=    3.194 closest distance to " O   HOH Z  80 " =    1.721
peak=    3.194 closest distance to " CG1 ILE A  20 " =    1.294
peak=    3.193 closest distance to " CB  ASN A 173 " =    1.080
peak=    3.190 closest distance to " CB  ALA A  43 " =    0.771
peak=    3.190 closest distance to " O   ASP A 191 " =    1.450
peak=    3.189 closest distance to " CA  ILE A 106 " =    0.822
peak=    3.189 closest distance to " C   ILE A 106 " =    1.900
peak=    3.188 closest distance to " O   HOH Z  59 " =    1.868
peak=    3.179 closest distance to " CG  ARG A 138 " =    1.285
peak=    3.179 closest distance to " O   HOH Z  88 " =    2.713
peak=    3.179 closest distance to " CG  ARG A 159 " =    0.893
peak=    3.179 closest distance to " CB  ALA A 299 " =    0.969
peak=    3.175 closest distance to " CG1 ILE A 151 " =    0.992
peak=    3.174 closest distance to " O   HOH Z  97 " =    2.472
peak=    3.169 closest distance to " CD1AILE A 234 " =    0.952
peak=    3.169 closest distance to " CB  GLN A  89 " =    1.323
peak=    3.166 closest distance to " CB  ARG A 156 " =    1.127
peak=    3.166 closest distance to " CA  MET A  40 " =    1.139
peak=    3.162 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.159 closest distance to " CA  ARG A 102 " =    1.135
peak=    3.158 closest distance to " O   HOH Z 273 " =    2.970
peak=    3.155 closest distance to " O   HOH Z 425 " =    1.274
peak=    3.153 closest distance to " CE3 TRP A 150 " =    1.088
peak=    3.152 closest distance to " CZ2 TRP A 179 " =    1.762
peak=    3.148 closest distance to " O   HOH Z 234 " =    1.833
peak=    3.147 closest distance to " O   HOH Z 261 " =    1.725
peak=    3.145 closest distance to " OE2 GLU A  53 " =    1.247
peak=    3.141 closest distance to " O   HOH Z 106 " =    4.161
peak=    3.139 closest distance to " OD2 ASP A 286 " =    3.276
peak=    3.138 closest distance to " OG BSER A  99 " =    2.313
peak=    3.132 closest distance to " O   ALA A 158 " =    1.260
peak=    3.129 closest distance to " O   HOH Z 422 " =    2.657
peak=    3.125 closest distance to " O   HOH Z 120 " =    3.425
peak=    3.120 closest distance to " O   HOH Z 116 " =    1.798
peak=    3.117 closest distance to " O  BHOH Z 338 " =    2.892
peak=    3.108 closest distance to " CB  ALA A   1 " =    4.822
peak=    3.107 closest distance to " CG2 ILE A 151 " =    1.008
peak=    3.106 closest distance to " CB  GLN A 103 " =    0.853
peak=    3.105 closest distance to " CB  SER A 216 " =    0.962
peak=    3.103 closest distance to " CG  MET A 185 " =    1.007
peak=    3.098 closest distance to " NH1BARG A 145 " =    0.973
peak=    3.098 closest distance to " O   HOH Z 332 " =    1.524
peak=    3.091 closest distance to " CD1 LEU A 261 " =    1.255
peak=    3.085 closest distance to " O   HOH Z  62 " =    2.058
peak=    3.082 closest distance to " O   HOH Z   9 " =    1.778
peak=    3.074 closest distance to " O   HOH Z 384 " =    3.083
peak=    3.073 closest distance to " CB  ARG A 102 " =    0.808
peak=    3.072 closest distance to " N   TYR A  15 " =    0.744
peak=    3.071 closest distance to " N   ALA A 256 " =    1.165
peak=    3.067 closest distance to " CA  ASP A 191 " =    1.258
peak=    3.064 closest distance to " O   HOH Z 421 " =    2.954
peak=    3.042 closest distance to " CB  ALA A 248 " =    0.951
peak=    3.029 closest distance to " CA  ALA A 299 " =    0.960

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.757
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 192
   mapped sites are within: 0.780 - 5.757

peak=   -4.943 closest distance to " CD  ARG A  14 " =    3.484
peak=   -4.611 closest distance to " CG1 VAL A 112 " =    2.657
peak=   -4.447 closest distance to " O   PRO A 198 " =    1.293
peak=   -4.439 closest distance to " CD  ARG A 156 " =    2.077
peak=   -4.388 closest distance to " CD  GLN A  58 " =    0.928
peak=   -4.272 closest distance to " O   HOH Z 231 " =    2.267
peak=   -4.191 closest distance to " O   HOH Z 377 " =    2.167
peak=   -4.144 closest distance to " CG1 VAL A 112 " =    2.882
peak=   -4.091 closest distance to " OG BSER A 134 " =    1.375
peak=   -4.061 closest distance to " CZ3 TRP A 179 " =    1.166
peak=   -4.030 closest distance to " O   HOH Z 211 " =    1.172
peak=   -4.014 closest distance to " CG1 VAL A  67 " =    2.980
peak=   -3.993 closest distance to " O   HOH Z 198 " =    1.812
peak=   -3.986 closest distance to " CD2 TYR A 293 " =    1.972
peak=   -3.983 closest distance to " C   HIS A 108 " =    1.105
peak=   -3.961 closest distance to " O   VAL A  67 " =    2.712
peak=   -3.948 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.943 closest distance to " O   HOH Z 266 " =    5.662
peak=   -3.934 closest distance to " O   HOH Z 196 " =    2.100
peak=   -3.929 closest distance to " OG  SER A  97 " =    2.313
peak=   -3.928 closest distance to " OD1 ASN A 148 " =    1.400
peak=   -3.926 closest distance to " O   HOH Z  73 " =    2.337
peak=   -3.913 closest distance to " CG1 VAL A 250 " =    2.682
peak=   -3.907 closest distance to " CB  ALA A  43 " =    2.650
peak=   -3.906 closest distance to " CB  PRO A 243 " =    2.723
peak=   -3.876 closest distance to " CD2 PHE A 192 " =    2.059
peak=   -3.863 closest distance to " CE2 PHE A  61 " =    2.668
peak=   -3.847 closest distance to " CG2 ILE A  49 " =    2.851
peak=   -3.843 closest distance to " CG  GLN A 223 " =    2.112
peak=   -3.837 closest distance to " O   HOH Z 394 " =    1.548
peak=   -3.826 closest distance to " CE BMET A  47 " =    1.524
peak=   -3.821 closest distance to " N   ALA A  43 " =    2.555
peak=   -3.750 closest distance to " O   HOH Z 185 " =    2.334
peak=   -3.730 closest distance to " O   HOH Z 372 " =    2.382
peak=   -3.727 closest distance to " O   ALA A  10 " =    1.655
peak=   -3.716 closest distance to " CA  GLY A 241 " =    3.472
peak=   -3.710 closest distance to " O   HOH Z 290 " =    1.287
peak=   -3.696 closest distance to " OXT GLY A 302 " =    3.030
peak=   -3.696 closest distance to " CE3 TRP A 150 " =    2.208
peak=   -3.691 closest distance to " O   TYR A 247 " =    2.884
peak=   -3.678 closest distance to " CA  ASP A 298 " =    1.112
peak=   -3.664 closest distance to " CB  GLN A  11 " =    1.718
peak=   -3.659 closest distance to " CE  MET A 105 " =    2.399
peak=   -3.639 closest distance to " CZ  PHE A 155 " =    1.264
peak=   -3.627 closest distance to " CB  HIS A  86 " =    1.136
peak=   -3.620 closest distance to " O   HOH Z  51 " =    1.684
peak=   -3.611 closest distance to " O   VAL A 189 " =    2.609
peak=   -3.605 closest distance to " CA  GLY A 203 " =    2.525
peak=   -3.600 closest distance to " CD1 LEU A 101 " =    2.419
peak=   -3.593 closest distance to " CB  ALA A 161 " =    2.547
peak=   -3.586 closest distance to " CB  ASN A  39 " =    2.250
peak=   -3.583 closest distance to " CA  GLY A 241 " =    2.375
peak=   -3.578 closest distance to " O   HOH Z  10 " =    1.530
peak=   -3.567 closest distance to " O   HOH Z 166 " =    1.967
peak=   -3.552 closest distance to " O   HOH Z  38 " =    1.548
peak=   -3.543 closest distance to " O   HOH Z 216 " =    1.135
peak=   -3.536 closest distance to " O   GLY A  17 " =    1.151
peak=   -3.533 closest distance to " ND2 ASN A  45 " =    1.958
peak=   -3.515 closest distance to " O   HOH Z 407 " =    3.132
peak=   -3.514 closest distance to " N   ALA A 248 " =    1.679
peak=   -3.504 closest distance to " NH2AARG A 275 " =    5.490
peak=   -3.497 closest distance to " ND2 ASN A  60 " =    1.375
peak=   -3.490 closest distance to " OD1 ASP A 171 " =    1.616
peak=   -3.481 closest distance to " ND2 ASN A 249 " =    2.452
peak=   -3.481 closest distance to " CG  ARG A 269 " =    2.550
peak=   -3.481 closest distance to " N   THR A  52 " =    1.662
peak=   -3.475 closest distance to " O   HOH Z 359 " =    3.034
peak=   -3.474 closest distance to " CG1BVAL A  41 " =    2.748
peak=   -3.474 closest distance to " O   VAL A 189 " =    1.625
peak=   -3.472 closest distance to " O   PHE A 218 " =    1.503
peak=   -3.466 closest distance to " CD1 LEU A 255 " =    2.980
peak=   -3.464 closest distance to " CB  ALA A 291 " =    2.252
peak=   -3.462 closest distance to " CG  GLU A 277 " =    1.240
peak=   -3.460 closest distance to " O   HOH Z 389 " =    2.113
peak=   -3.458 closest distance to " CG  PRO A 198 " =    1.904
peak=   -3.452 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.443 closest distance to " CG1 VAL A 125 " =    1.798
peak=   -3.437 closest distance to " CB  ALA A 129 " =    2.449
peak=   -3.436 closest distance to " O   HOH Z 174 " =    3.907
peak=   -3.431 closest distance to " CA  SER A 135 " =    1.259
peak=   -3.428 closest distance to " NH2 ARG A  79 " =    1.507
peak=   -3.424 closest distance to " O   HOH Z 345 " =    2.165
peak=   -3.423 closest distance to " O   HOH Z  37 " =    1.834
peak=   -3.412 closest distance to " O   HOH Z 351 " =    1.492
peak=   -3.408 closest distance to " CB  ALA A 291 " =    2.323
peak=   -3.407 closest distance to " O   HOH Z 174 " =    2.687
peak=   -3.405 closest distance to " CB  ALA A 100 " =    2.216
peak=   -3.392 closest distance to " C   MET A 188 " =    1.333
peak=   -3.390 closest distance to " C   LEU A 143 " =    1.096
peak=   -3.385 closest distance to " CB  TRP A  85 " =    2.561
peak=   -3.377 closest distance to " CG2 ILE A 263 " =    2.375
peak=   -3.372 closest distance to " O   HOH Z 275 " =    1.509
peak=   -3.370 closest distance to " O   HOH Z  60 " =    2.282
peak=   -3.368 closest distance to " O   HOH Z 313 " =    1.882
peak=   -3.365 closest distance to " CG  MET A 105 " =    0.988
peak=   -3.363 closest distance to " NE2 GLN A 194 " =    1.949
peak=   -3.359 closest distance to " OH  TYR A 247 " =    2.141
peak=   -3.358 closest distance to " O   HOH Z 128 " =    2.638
peak=   -3.357 closest distance to " CB  ASP A 286 " =    2.138
peak=   -3.349 closest distance to " O   PRO A 163 " =    1.996
peak=   -3.342 closest distance to " CD1 PHE A  59 " =    1.994
peak=   -3.339 closest distance to " O   HOH Z 295 " =    1.720
peak=   -3.338 closest distance to " O   GLN A 240 " =    2.172
peak=   -3.335 closest distance to " CD2 PHE A  61 " =    2.099
peak=   -3.335 closest distance to " O   TRP A  70 " =    1.439
peak=   -3.335 closest distance to " C   ASN A 285 " =    2.410
peak=   -3.334 closest distance to " CB  ALA A 248 " =    2.446
peak=   -3.321 closest distance to " O   ARG A  24 " =    1.747
peak=   -3.321 closest distance to " O   HOH Z 348 " =    2.204
peak=   -3.317 closest distance to " OE1 GLN A  88 " =    1.117
peak=   -3.313 closest distance to " O   HOH Z 114 " =    3.059
peak=   -3.313 closest distance to " O   SER A 210 " =    1.955
peak=   -3.312 closest distance to " CG2 THR A 178 " =    2.264
peak=   -3.306 closest distance to " OD2 ASP A 191 " =    1.493
peak=   -3.305 closest distance to " CG  PHE A 283 " =    2.649
peak=   -3.302 closest distance to " O   HOH Z 326 " =    5.126
peak=   -3.301 closest distance to " CD1 LEU A   5 " =    2.590
peak=   -3.300 closest distance to " O   ALA A 180 " =    1.412
peak=   -3.300 closest distance to " CG  ASP A 132 " =    2.338
peak=   -3.299 closest distance to " CA  GLY A 133 " =    2.297
peak=   -3.296 closest distance to " CD  ARG A  79 " =    1.194
peak=   -3.291 closest distance to " O   HOH Z  52 " =    1.588
peak=   -3.289 closest distance to " C   SER A 206 " =    1.493
peak=   -3.285 closest distance to " O   HOH Z 134 " =    3.142
peak=   -3.285 closest distance to " O   HOH Z 176 " =    0.823
peak=   -3.274 closest distance to " O   GLY A 211 " =    1.338
peak=   -3.269 closest distance to " CD2 HIS A 207 " =    2.202
peak=   -3.267 closest distance to " O   ILE A 106 " =    1.949
peak=   -3.266 closest distance to " O   HOH Z 111 " =    3.929
peak=   -3.264 closest distance to " O   ALA A  34 " =    2.459
peak=   -3.258 closest distance to " NE2 GLN A  88 " =    1.943
peak=   -3.256 closest distance to " O   HOH Z 281 " =    2.669
peak=   -3.253 closest distance to " O   TYR A 186 " =    1.683
peak=   -3.252 closest distance to " CG  TRP A 266 " =    1.849
peak=   -3.252 closest distance to " O   HOH Z 298 " =    1.296
peak=   -3.248 closest distance to " O   HOH Z 421 " =    3.138
peak=   -3.246 closest distance to " O   HOH Z 311 " =    3.810
peak=   -3.243 closest distance to " CZ  PHE A  38 " =    2.052
peak=   -3.238 closest distance to " N   THR A 157 " =    1.609
peak=   -3.236 closest distance to " ND2 ASN A  45 " =    1.130
peak=   -3.235 closest distance to " CA  GLY A 241 " =    2.888
peak=   -3.233 closest distance to " CG  LEU A  83 " =    1.994
peak=   -3.233 closest distance to " CD  ARG A 139 " =    1.622
peak=   -3.231 closest distance to " C   PHE A  59 " =    1.366
peak=   -3.230 closest distance to " O   HOH Z  63 " =    1.785
peak=   -3.228 closest distance to " O   HOH Z  11 " =    1.633
peak=   -3.227 closest distance to " C   ALA A 158 " =    1.473
peak=   -3.223 closest distance to " CG2 THR A 178 " =    2.388
peak=   -3.222 closest distance to " O   HOH Z 393 " =    1.385
peak=   -3.218 closest distance to " O   HOH Z 429 " =    1.920
peak=   -3.216 closest distance to " CB  ALA A   7 " =    2.304
peak=   -3.210 closest distance to " CA  GLY A 287 " =    1.520
peak=   -3.207 closest distance to " NE2 GLN A 278 " =    1.523
peak=   -3.204 closest distance to " O   HOH Z 111 " =    1.786
peak=   -3.204 closest distance to " CE3 TRP A 274 " =    2.438
peak=   -3.201 closest distance to " O   ARG A 145 " =    1.606
peak=   -3.199 closest distance to " O   HOH Z 351 " =    1.510
peak=   -3.195 closest distance to " CB  PRO A 163 " =    2.495
peak=   -3.191 closest distance to " OD2 ASP A 171 " =    1.889
peak=   -3.182 closest distance to " CD  GLU A 236 " =    1.114
peak=   -3.179 closest distance to " CD  GLN A 223 " =    0.939
peak=   -3.179 closest distance to " O   HOH Z  64 " =    1.473
peak=   -3.177 closest distance to " O   HOH Z   6 " =    1.418
peak=   -3.175 closest distance to " CG2 VAL A 189 " =    2.121
peak=   -3.173 closest distance to " O   HOH Z 298 " =    2.509
peak=   -3.170 closest distance to " O   HOH Z 191 " =    5.757
peak=   -3.166 closest distance to " O   SER A 135 " =    1.444
peak=   -3.166 closest distance to " CA  ILE A 263 " =    1.175
peak=   -3.164 closest distance to " C   LEU A 222 " =    0.780
peak=   -3.161 closest distance to " CB  PHE A  16 " =    2.501
peak=   -3.155 closest distance to " OD1 ASN A 187 " =    1.579
peak=   -3.153 closest distance to " O   HOH Z 252 " =    4.006
peak=   -3.149 closest distance to " C   GLY A 262 " =    2.024
peak=   -3.148 closest distance to " O   HOH Z 171 " =    1.958
peak=   -3.136 closest distance to " CB  ALA A  10 " =    2.270
peak=   -3.131 closest distance to " O   HOH Z  60 " =    1.398
peak=   -3.119 closest distance to " CD1 TRP A  70 " =    1.078
peak=   -3.116 closest distance to " CD2 TYR A 247 " =    2.423
peak=   -3.115 closest distance to " CG1AVAL A  41 " =    2.883
peak=   -3.108 closest distance to " CA  TRP A 274 " =    1.212
peak=   -3.106 closest distance to " O   HOH Z  71 " =    2.468
peak=   -3.101 closest distance to " O   HOH Z 357 " =    2.170
peak=   -3.096 closest distance to " O   ALA A 180 " =    1.023
peak=   -3.095 closest distance to " O   GLU A 152 " =    1.338
peak=   -3.090 closest distance to " O   HOH Z  90 " =    1.828
peak=   -3.087 closest distance to " O   HOH Z 247 " =    1.962
peak=   -3.081 closest distance to " O   GLN A 240 " =    2.614
peak=   -3.074 closest distance to " N   GLN A 223 " =    0.984
peak=   -3.060 closest distance to " CG1 VAL A  67 " =    3.053
peak=   -3.044 closest distance to " CA  GLY A  57 " =    2.071
peak=   -3.025 closest distance to " OD1AASN A 224 " =    1.754
peak=   -3.020 closest distance to " O   HOH Z  70 " =    2.148

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.3641 0.3553   6.150827e+00   6.130553e+00
   1_bss:  0.3446 0.3405   6.123793e+00   6.103069e+00
   1_xyz:  0.2350 0.2631   5.761415e+00   5.845299e+00
   1_adp:  0.2157 0.2677   5.710609e+00   5.860083e+00
   1_occ:  0.2153 0.2677   5.710200e+00   5.860930e+00
   2_bss:  0.2114 0.2643   5.698186e+00   5.853474e+00
   2_xyz:  0.1516 0.1961   5.390929e+00   5.585762e+00
   2_adp:  0.1376 0.1838   5.311591e+00   5.527866e+00
   2_occ:  0.1374 0.1836   5.311169e+00   5.527792e+00
   3_bss:  0.1368 0.1822   5.305386e+00   5.521436e+00
   3_xyz:  0.1208 0.1681   5.206641e+00   5.441387e+00
   3_adp:  0.1186 0.1640   5.188333e+00   5.420674e+00
   3_occ:  0.1185 0.1638   5.187842e+00   5.420463e+00
   4_bss:  0.1183 0.1637   5.187188e+00   5.420441e+00
   4_xyz:  0.1138 0.1618   5.163524e+00   5.408053e+00
   4_adp:  0.1148 0.1610   5.166525e+00   5.404937e+00
   4_occ:  0.1146 0.1608   5.165615e+00   5.404546e+00
   5_bss:  0.1145 0.1597   5.161965e+00   5.398921e+00
   5_xyz:  0.1168 0.1608   5.178994e+00   5.410342e+00
   5_adp:  0.1151 0.1622   5.174741e+00   5.416185e+00
   5_occ:  0.1150 0.1622   5.174837e+00   5.416484e+00
   5_bss:  0.1149 0.1620   5.174952e+00   5.416580e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.313  56.573  -2.935  -3.221   6.276  -0.000   0.000   0.000
   1_xyz:  0.313  56.573  -2.935  -3.221   6.276  -0.000   0.000   0.000
   1_adp:  0.313  56.573  -2.935  -3.221   6.276  -0.000   0.000   0.000
   1_occ:  0.313  56.573  -2.935  -3.221   6.276  -0.000   0.000   0.000
   2_bss:  0.335  71.972  -2.789  -2.590   1.588  -0.000   0.000   0.000
   2_xyz:  0.335  71.972  -2.789  -2.590   1.588  -0.000   0.000   0.000
   2_adp:  0.335  71.972  -2.789  -2.590   1.588  -0.000   0.000   0.000
   2_occ:  0.335  71.972  -2.789  -2.590   1.588  -0.000   0.000   0.000
   3_bss:  0.337  76.877  -2.682  -2.399   0.192  -0.000   0.000   0.000
   3_xyz:  0.337  76.877  -2.682  -2.399   0.192  -0.000   0.000   0.000
   3_adp:  0.337  76.877  -2.682  -2.399   0.192  -0.000   0.000   0.000
   3_occ:  0.337  76.877  -2.682  -2.399   0.192  -0.000   0.000   0.000
   4_bss:  0.327  65.714  -2.396  -2.192  -0.078  -0.000  -0.000  -0.000
   4_xyz:  0.327  65.714  -2.396  -2.192  -0.078  -0.000  -0.000  -0.000
   4_adp:  0.327  65.714  -2.396  -2.192  -0.078  -0.000  -0.000  -0.000
   4_occ:  0.327  65.714  -2.396  -2.192  -0.078  -0.000  -0.000  -0.000
   5_bss:  0.329  65.714  -2.449  -2.245  -0.273  -0.000  -0.000  -0.000
   5_xyz:  0.329  65.714  -2.449  -2.245  -0.273  -0.000  -0.000  -0.000
   5_adp:  0.329  65.714  -2.449  -2.245  -0.273  -0.000  -0.000  -0.000
   5_occ:  0.329  65.714  -2.449  -2.245  -0.273  -0.000  -0.000  -0.000
   5_bss:  0.329  65.705  -2.213  -2.014  -0.110  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.940 0.6580  0.8122    38276.129
   1_bss:  37.665 0.6717  0.8307    35044.395
   1_xyz:  26.082 0.8012  0.9629    17939.682
   1_adp:  26.700 0.7941  0.9602    18595.183
   1_occ:  26.746 0.7935  0.9593    18632.716
   2_bss:  26.025 0.8018  0.9293    18206.750
   2_xyz:  18.702 0.8735  0.9750     9700.749
   2_adp:  17.171 0.8878  0.9741     8619.894
   2_occ:  17.169 0.8878  0.9740     8611.067
   3_bss:  16.994 0.8893  0.9628     8469.876
   3_xyz:  15.124 0.9055  0.9705     7115.872
   3_adp:  14.602 0.9103  0.9655     6838.096
   3_occ:  14.599 0.9103  0.9654     6832.967
   4_bss:  14.594 0.9104  0.9682     6831.195
   4_xyz:  14.323 0.9127  0.9710     6676.379
   4_adp:  14.229 0.9136  0.9672     6656.843
   4_occ:  14.223 0.9136  0.9672     6644.430
   5_bss:  14.133 0.9142  0.9641     6505.906
   5_xyz:  14.305 0.9130  0.9623     6644.094
   5_adp:  14.460 0.9117  0.9548     6683.111
   5_occ:  14.462 0.9117  0.9546     6685.888
   5_bss:  14.464 0.9117  0.9614     6687.783
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6766e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6766e-01
   1_xyz:   1.317  0.010  0.083 15.532  0.006  4.114   9.4918e-02
   1_adp:   1.317  0.010  0.083 15.532  0.006  4.114   9.4918e-02
   1_occ:   1.317  0.010  0.083 15.532  0.006  4.114   9.4918e-02
   2_bss:   1.317  0.010  0.083 15.532  0.006  4.114   9.4918e-02
   2_xyz:   1.112  0.009  0.081 15.173  0.004  4.133   7.3470e-02
   2_adp:   1.112  0.009  0.081 15.173  0.004  4.133   7.3470e-02
   2_occ:   1.112  0.009  0.081 15.173  0.004  4.133   7.3470e-02
   3_bss:   1.112  0.009  0.081 15.173  0.004  4.133   7.3470e-02
   3_xyz:   1.110  0.010  0.082 15.022  0.004  4.129   7.2906e-02
   3_adp:   1.110  0.010  0.082 15.022  0.004  4.129   7.2906e-02
   3_occ:   1.110  0.010  0.082 15.022  0.004  4.129   7.2906e-02
   4_bss:   1.110  0.010  0.082 15.022  0.004  4.129   7.2906e-02
   4_xyz:   1.121  0.011  0.086 15.005  0.004  4.116   7.8019e-02
   4_adp:   1.121  0.011  0.086 15.005  0.004  4.116   7.8019e-02
   4_occ:   1.121  0.011  0.086 15.005  0.004  4.116   7.8019e-02
   5_bss:   1.121  0.011  0.086 15.005  0.004  4.116   7.8019e-02
   5_xyz:   0.997  0.008  0.077 14.723  0.003  4.117   6.1208e-02
   5_adp:   0.997  0.008  0.077 14.723  0.003  4.117   6.1208e-02
   5_occ:   0.997  0.008  0.077 14.723  0.003  4.117   6.1208e-02
   5_bss:   0.997  0.008  0.077 14.723  0.003  4.117   6.1208e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.553   2.4395e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.553   2.4395e-01
   1_xyz:   8.879  0.050  0.305 82.473  0.039  2.126   1.1943e-01
   1_adp:   8.879  0.050  0.305 82.473  0.039  2.126   1.1943e-01
   1_occ:   8.879  0.050  0.305 82.473  0.039  2.126   1.1943e-01
   2_bss:   8.879  0.050  0.305 82.473  0.039  2.126   1.1943e-01
   2_xyz:   6.653  0.051  0.241 86.240  0.044  2.330   1.2018e-01
   2_adp:   6.653  0.051  0.241 86.240  0.044  2.330   1.2018e-01
   2_occ:   6.653  0.051  0.241 86.240  0.044  2.330   1.2018e-01
   3_bss:   6.653  0.051  0.241 86.240  0.044  2.330   1.2018e-01
   3_xyz:   7.433  0.055  0.267 82.701  0.038  2.357   5.1180e-02
   3_adp:   7.433  0.055  0.267 82.701  0.038  2.357   5.1180e-02
   3_occ:   7.433  0.055  0.267 82.701  0.038  2.357   5.1180e-02
   4_bss:   7.433  0.055  0.267 82.701  0.038  2.357   5.1180e-02
   4_xyz:   7.316  0.060  0.286 82.901  0.037  2.292   6.2564e-02
   4_adp:   7.316  0.060  0.286 82.901  0.037  2.292   6.2564e-02
   4_occ:   7.316  0.060  0.286 82.901  0.037  2.292   6.2564e-02
   5_bss:   7.316  0.060  0.286 82.901  0.037  2.292   6.2564e-02
   5_xyz:   6.841  0.047  0.233 82.481  0.033  2.385   4.1804e-02
   5_adp:   6.841  0.047  0.233 82.481  0.033  2.385   4.1804e-02
   5_occ:   6.841  0.047  0.233 82.481  0.033  2.385   4.1804e-02
   5_bss:   6.841  0.047  0.233 82.481  0.033  2.385   4.1804e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 114.25   0.00  16.97 114.25   0.00  13.09  64.33   3.40  38.09
   1_occ: 114.25   0.00  16.97 114.25   0.00  13.09  64.33   3.40  38.09
   2_bss: 114.25   0.00  16.97 114.25   0.00  13.09  64.33   3.40  38.09
   2_xyz: 114.25   0.00  16.97 114.25   0.00  13.09  64.33   3.40  38.09
   2_adp:  83.25   0.00  17.63  76.74   0.00  13.10  83.25   4.95  42.26
   2_occ:  83.25   0.00  17.63  76.74   0.00  13.10  83.25   4.95  42.26
   3_bss:  83.25   0.00  17.63  76.74   0.00  13.10  83.25   4.95  42.26
   3_xyz:  83.25   0.00  17.63  76.74   0.00  13.10  83.25   4.95  42.26
   3_adp:  83.54   1.01  17.05  78.64   1.01  12.78  83.54   3.44  40.34
   3_occ:  83.54   1.01  17.05  78.64   1.01  12.78  83.54   3.44  40.34
   4_bss:  83.54   1.01  17.05  78.64   1.01  12.78  83.54   3.44  40.34
   4_xyz:  83.54   1.01  17.05  78.64   1.01  12.78  83.54   3.44  40.34
   4_adp:  80.54   1.35  16.44  75.10   1.71  12.54  80.54   1.35  37.69
   4_occ:  80.54   1.35  16.44  75.10   1.71  12.54  80.54   1.35  37.69
   5_bss:  80.54   1.35  16.44  75.10   1.71  12.54  80.54   1.35  37.69
   5_xyz:  80.54   1.35  16.44  75.10   1.71  12.54  80.54   1.35  37.69
   5_adp:  90.18   0.30  16.83  85.47   0.30  12.59  90.18   0.44  39.96
   5_occ:  90.18   0.30  16.83  85.47   0.30  12.59  90.18   0.44  39.96
   5_bss:  90.17   0.29  16.83  85.46   0.29  12.58  90.17   0.43  39.95
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.471    0.022    0.347
   1_adp:    1.471    0.022    0.347
   1_occ:    1.471    0.022    0.347
   2_bss:    1.471    0.022    0.347
   2_xyz:    1.224    0.029    0.442
   2_adp:    1.224    0.029    0.442
   2_occ:    1.224    0.029    0.442
   3_bss:    1.224    0.029    0.442
   3_xyz:    1.154    0.024    0.477
   3_adp:    1.154    0.024    0.477
   3_occ:    1.154    0.024    0.477
   4_bss:    1.154    0.024    0.477
   4_xyz:    1.327    0.026    0.494
   4_adp:    1.327    0.026    0.494
   4_occ:    1.327    0.026    0.494
   5_bss:    1.327    0.026    0.494
   5_xyz:    1.525    0.034    0.499
   5_adp:    1.525    0.034    0.499
   5_occ:    1.525    0.034    0.499
   5_bss:    1.525    0.034    0.499
------------------------------------------------------------------------

CPU time actual refinement: 322.62


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_791/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 322.48 
  Macro-tasks:
    bulk solvent and scale       = 44.19  
    individual site refinement   = 125.20 
    weights calculation          = 30.09  
    collect and process          = 6.67   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.26 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 98.88  
    alpha_beta                      = 8.12   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 106.42 
    fmodel                         = 7.29   
    r_factors                      = 0.25   
    phase_errors                   = 11.14  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 235.34 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.646 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    617 calls, 98.47 s
gradients_fft:          562 calls, 93.62 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 05:40:22 PST -0800 (1200490822.09 s)
Start R-work = 0.3641, R-free = 0.3553 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1798 (no bulk solvent and anisotropic scale)

Start R-work = 0.3446, R-free = 0.3405
Final R-work = 0.1149, R-free = 0.1620