# Date 2008-01-16 Time 05:00:08 PST -0800 (1200488408.22 s)
#phil __OFF__

Command line arguments: "../548.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7319
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 548

-------------------------------------------------------------------------------
  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: (69.8988, 46.93, 88.1178, 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: 3.25, 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: (69.8988, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99071
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955049

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9907

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: (69.8988, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99071
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955049

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2593 [2152/2176]  1933   219  10.2%
  bin  2:  4.2593 -  3.3936 [2059/2078]  1856   203   9.9%
  bin  3:  3.3936 -  2.9684 [2036/2055]  1834   202   9.9%
  bin  4:  2.9684 -  2.6987 [2012/2042]  1807   205  10.2%
  bin  5:  2.6987 -  2.5062 [2011/2030]  1811   200   9.9%
  bin  6:  2.5062 -  2.3590 [2000/2025]  1799   201  10.1%
  bin  7:  2.3590 -  2.2413 [1990/2018]  1795   195   9.8%
  bin  8:  2.2413 -  2.1440 [1975/2011]  1772   203  10.3%
  bin  9:  2.1440 -  2.0617 [1965/2007]  1776   189   9.6%
  bin 10:  2.0617 -  1.9907 [1389/2005]  1247   142  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_548/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:
        1.60 -     2.26: 12
        2.26 -     2.92: 1469
        2.92 -     3.58: 4413
        3.58 -     4.24: 9119
        4.24 -     4.90: 13075
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.597 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.618 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.770 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.912 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28083 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_548/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_548/model_refine_001.geo

CPU time processing inputs: 8.98


============================ 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 = 69.89875 46.93 88.1178 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: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3292   r_free= 0.3234   ksol= 0.00   Bsol= 0.00   scale= 0.958    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.073253                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7504 0.99   1397  153 0.2822 0.2805      6.3657      6.2694|
|  2:  4.7504 -  3.7905 0.99   1340  153 0.2520 0.2705      6.4545      6.5284|
|  3:  3.7905 -  3.3173 0.99   1311  146 0.2997 0.2672      6.4249      6.3476|
|  4:  3.3173 -  3.0166 0.99   1308  139 0.3042 0.3374      6.2756       6.326|
|  5:  3.0166 -  2.8019 0.99   1306  146 0.3399 0.2793      6.1429      6.0446|
|  6:  2.8019 -  2.6377 0.99   1292  148 0.3376 0.3854       6.039      6.0488|
|  7:  2.6377 -  2.5062 0.99   1287  144 0.3389 0.3182      6.0099      5.9624|
|  8:  2.5062 -  2.3976 0.98   1282  138 0.3797 0.3381      6.0449      5.9726|
|  9:  2.3976 -  2.3056 0.98   1276  147 0.3569 0.3532      5.9229      5.9544|
| 10:  2.3056 -  2.2263 0.99   1274  139 0.3857 0.3749      5.9747      5.8808|
| 11:  2.2263 -  2.1569 0.98   1268  139 0.3879 0.3749      5.8983       5.897|
| 12:  2.1569 -  2.0954 0.97   1257  141 0.3806 0.3553      5.8248      5.8733|
| 13:  2.0954 -  2.0404 1.00   1278  141 0.3840 0.4035      5.7417      5.7571|
| 14:  2.0404 -  1.9907 0.58    754   85 0.3405 0.3460       5.677      5.5841|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7504  1397   153  0.80  24.74   0.86     0.82      39873.03|
|  2:  4.7504 -  3.7905  1340   153  0.84  22.59   0.97     0.91      49110.24|
|  3:  3.7905 -  3.3173  1311   146  0.80  26.77   0.96     0.93      48130.01|
|  4:  3.3173 -  3.0166  1308   139  0.77  29.61   0.97     0.89      41675.99|
|  5:  3.0166 -  2.8019  1306   146  0.71  34.39   0.99     0.86      33195.75|
|  6:  2.8019 -  2.6377  1292   148  0.70  35.90   0.98     0.85      30308.25|
|  7:  2.6377 -  2.5062  1287   144  0.70  36.06   1.00     0.86      27565.99|
|  8:  2.5062 -  2.3976  1282   138  0.70  35.92   0.97     0.87      25076.66|
|  9:  2.3976 -  2.3056  1276   147  0.70  35.89   1.01     0.89      23331.41|
| 10:  2.3056 -  2.2263  1274   139  0.68  37.77   1.03     0.88      22237.58|
| 11:  2.2263 -  2.1569  1268   139  0.66  38.91   1.00     0.91      23093.57|
| 12:  2.1569 -  2.0954  1257   141  0.65  39.86   1.03     0.91      21795.47|
| 13:  2.0954 -  2.0404  1278   141  0.62  42.33   1.01     0.87      19949.96|
| 14:  2.0404 -  1.9907   754    85  0.63  42.15   1.05     0.78      16965.89|
|alpha:            min =        0.78 max =            0.93 mean =         0.88|
|beta:             min =    16965.89 max =        49110.24 mean =     30761.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.71|
|phase err.(work): min =        0.00 max =           89.99 mean =        34.13|
|phase err.(test): min =        0.00 max =           89.95 mean =        34.05|
|-----------------------------------------------------------------------------|

============================== 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 = 3.248188              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.396   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633067              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.326   (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 |  1.597 -  1.927:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.927 -  2.258:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.258 -  2.588:       24 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.588 -  2.918:     1445 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.918 -  3.248:     1871 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.248 -  3.579:     2542 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.579 -  3.909:     4680 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.909 -  4.239:     4439 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.239 -  4.570:     5976 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.570 -  4.900:     7099 |
|-----------------------------------------------------------------------------|
|-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 |   4.113    4.900  1.597 |       0.250 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    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: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3292   r_free= 0.3234   ksol= 0.00   Bsol= 0.00   scale= 0.958    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.073253                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3099   r_free= 0.3065   ksol= 0.32   Bsol= 49.30   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-3.07,4.60,-0.00,0.00,0.00); trace/3= -0.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.040525                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.821871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.174   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.364409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.057   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3099      final r-factor (work) = 0.2108          |
| start r-factor (free) = 0.3065      final r-factor (free) = 0.2345          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6959 = 2.82 * 0.50 * 6.0439 + 1.00 * 0.1683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2389 = 2.82 * 0.50 * 5.7899 + 1.00 * 0.0697                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2108      final r-factor (work) = 0.1975          |
| start r-factor (free) = 0.2345      final r-factor (free) = 0.2358          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1171 = 0.36 * 1.00 * 5.7899 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1852 = 0.36 * 1.00 * 5.6159 + 1.00 * 0.1387                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.29   16.28    None  None   None       |
|    all(noH): 2823   0      0.00    89.29   16.28    None  None   None       |
|    Sol.    : 438    0      4.14    62.78   37.12    None  None   None       |
|    Mac.    : 2385   0      0.00    89.29   12.45    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 -   8.929:  701   |   5:    44.645 -  53.574:   98        |
|      1:     8.929 -  17.858: 1408   |   6:    53.574 -  62.503:   44        |
|      2:    17.858 -  26.787:  288   |   7:    62.503 -  71.432:    1        |
|      3:    26.787 -  35.716:  152   |   8:    71.432 -  80.361:    0        |
|      4:    35.716 -  44.645:  130   |   9:    80.361 -  89.290:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1975 r_free = 0.2358             target_work(ml) = 5.619         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1970 r_free = 0.2356             target_work(ml) = 5.618         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1970   r_free= 0.2356   ksol= 0.32   Bsol= 49.30   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-3.07,4.60,-0.00,0.00,0.00); trace/3= -0.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.617682                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1937   r_free= 0.2334   ksol= 0.33   Bsol= 60.59   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.57,0.94,-0.00,0.00,0.00); trace/3= -1.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.605874                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.351713              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.892   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.939536              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.562   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1937      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.2334      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2862 = 4.35 * 0.50 * 5.6146 + 1.00 * 0.0697                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9091 = 4.35 * 0.50 * 5.4414 + 1.00 * 0.0694                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1337      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1557 = 0.94 * 1.00 * 5.4414 + 1.00 * 0.0434                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9200 = 0.94 * 1.00 * 5.2258 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.10   17.15    None  None   None       |
|    all(noH): 2823   0      0.00    81.10   17.15    None  None   None       |
|    Sol.    : 438    0      5.74    80.84   40.98    None  None   None       |
|    Mac.    : 2385   0      0.00    81.10   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:     0.000 -   8.110:  649   |   5:    40.552 -  48.662:   98        |
|      1:     8.110 -  16.221: 1335   |   6:    48.662 -  56.772:   78        |
|      2:    16.221 -  24.331:  322   |   7:    56.772 -  64.883:   71        |
|      3:    24.331 -  32.441:  128   |   8:    64.883 -  72.993:   28        |
|      4:    32.441 -  40.552:  104   |   9:    72.993 -  81.103:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1227 r_free = 0.1683             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1226 r_free = 0.1681             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1681   ksol= 0.33   Bsol= 60.59   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.57,0.94,-0.00,0.00,0.00); trace/3= -1.57                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.216282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1674   ksol= 0.33   Bsol= 64.15   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.17,0.12,-0.00,0.00,0.00); trace/3= -1.58                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211971                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.611990              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.634  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.241118              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.729  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2802 = 1.61 * 0.50 * 5.2244 + 1.00 * 0.0694                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2438 = 1.61 * 0.50 * 5.2007 + 1.00 * 0.0520                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2641 = 0.24 * 1.00 * 5.2007 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2585 = 0.24 * 1.00 * 5.1836 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    80.93   16.60    None  None   None       |
|    all(noH): 2823   0      0.81    80.93   16.60    None  None   None       |
|    Sol.    : 438    0      3.19    80.73   38.90    None  None   None       |
|    Mac.    : 2385   0      0.81    80.93   12.51    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:     0.813 -   8.825:  821   |   5:    40.871 -  48.883:   91        |
|      1:     8.825 -  16.836: 1214   |   6:    48.883 -  56.894:   81        |
|      2:    16.836 -  24.848:  296   |   7:    56.894 -  64.906:   43        |
|      3:    24.848 -  32.860:  131   |   8:    64.906 -  72.917:   21        |
|      4:    32.860 -  40.871:  120   |   9:    72.917 -  80.929:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1178 r_free = 0.1604             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1177 r_free = 0.1603             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1603   ksol= 0.33   Bsol= 64.15   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.17,0.12,-0.00,0.00,0.00); trace/3= -1.58                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178655                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1602   ksol= 0.33   Bsol= 58.50   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.94,-0.04,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178435                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.723771              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.557  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.152213              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.235  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1113 = 2.72 * 0.50 * 5.1835 + 1.00 * 0.0520                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0853 = 2.72 * 0.50 * 5.1507 + 1.00 * 0.0706                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7926 = 0.15 * 1.00 * 5.1507 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7903 = 0.15 * 1.00 * 5.1421 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.08   16.19    None  None   None       |
|    all(noH): 2823   0      0.00    79.08   16.19    None  None   None       |
|    Sol.    : 438    0      0.00    78.62   37.48    None  None   None       |
|    Mac.    : 2385   0      1.48    79.08   12.28    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 -   7.908:  600   |   5:    39.540 -  47.448:   85        |
|      1:     7.908 -  15.816: 1394   |   6:    47.448 -  55.356:   84        |
|      2:    15.816 -  23.724:  333   |   7:    55.356 -  63.264:   42        |
|      3:    23.724 -  31.632:  131   |   8:    63.264 -  71.172:   16        |
|      4:    31.632 -  39.540:  133   |   9:    71.172 -  79.080:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1563             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1562             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1562   ksol= 0.33   Bsol= 58.50   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.94,-0.04,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1562   ksol= 0.33   Bsol= 58.50   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.83,-0.06,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.155845              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.930  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.358621              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.416  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1842 = 3.16 * 0.50 * 5.1420 + 1.00 * 0.0706                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1711 = 3.16 * 0.50 * 5.1313 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9791 = 1.36 * 1.00 * 5.1313 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9717 = 1.36 * 1.00 * 5.1245 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.24   16.34    None  None   None       |
|    all(noH): 2823   0      0.00    83.24   16.34    None  None   None       |
|    Sol.    : 438    0      0.00    80.25   38.88    None  None   None       |
|    Mac.    : 2385   0      0.20    83.24   12.20    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 -   8.324:  788   |   5:    41.621 -  49.945:  102        |
|      1:     8.324 -  16.648: 1259   |   6:    49.945 -  58.269:   79        |
|      2:    16.648 -  24.972:  288   |   7:    58.269 -  66.593:   36        |
|      3:    24.972 -  33.296:  127   |   8:    66.593 -  74.917:   18        |
|      4:    33.296 -  41.621:  122   |   9:    74.917 -  83.241:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1573             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1573             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1573   ksol= 0.33   Bsol= 58.50   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.83,-0.06,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.130504                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7504 0.99   1397  153 0.1020 0.1331      5.4303      5.5494|
|  2:  4.7504 -  3.7905 0.99   1340  153 0.0846 0.1129      5.4411       5.646|
|  3:  3.7905 -  3.3173 0.99   1311  146 0.1018 0.1524      5.4524      5.8475|
|  4:  3.3173 -  3.0166 0.99   1308  139 0.1158 0.1530      5.4179      5.5621|
|  5:  3.0166 -  2.8019 0.99   1306  146 0.1266 0.1612      5.2967       5.527|
|  6:  2.8019 -  2.6377 0.99   1292  148 0.1185 0.1991      5.1959      5.4989|
|  7:  2.6377 -  2.5062 0.99   1287  144 0.1221 0.1627      5.1541      5.3262|
|  8:  2.5062 -  2.3976 0.98   1282  138 0.1105 0.1614      5.0578       5.312|
|  9:  2.3976 -  2.3056 0.98   1276  147 0.1144 0.1853      5.0219      5.3218|
| 10:  2.3056 -  2.2263 0.99   1274  139 0.1078 0.1679      4.9279      5.1635|
| 11:  2.2263 -  2.1569 0.98   1268  139 0.1082 0.1717      4.9184      5.2031|
| 12:  2.1569 -  2.0954 0.97   1257  141 0.1099 0.1719       4.863      5.2686|
| 13:  2.0954 -  2.0404 1.00   1278  141 0.1028 0.1734      4.7612      5.0051|
| 14:  2.0404 -  1.9907 0.58    754   85 0.0879 0.1702      4.6031      4.9261|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7504  1397   153  0.93   9.91   0.97     0.94       8117.00|
|  2:  4.7504 -  3.7905  1340   153  0.95   8.02   1.01     0.99       9384.33|
|  3:  3.7905 -  3.3173  1311   146  0.94  10.95   1.02     1.01      10020.00|
|  4:  3.3173 -  3.0166  1308   139  0.92  13.08   1.00     0.99       9753.57|
|  5:  3.0166 -  2.8019  1306   146  0.91  15.34   0.99     0.96       7956.61|
|  6:  2.8019 -  2.6377  1292   148  0.90  16.08   0.97     0.95       6990.38|
|  7:  2.6377 -  2.5062  1287   144  0.91  15.53   0.98     0.95       6200.41|
|  8:  2.5062 -  2.3976  1282   138  0.91  14.88   0.98     0.96       5326.79|
|  9:  2.3976 -  2.3056  1276   147  0.91  15.50   0.99     0.95       5005.01|
| 10:  2.3056 -  2.2263  1274   139  0.90  15.59   0.99     0.95       4224.07|
| 11:  2.2263 -  2.1569  1268   139  0.90  15.93   0.98     0.95       4340.10|
| 12:  2.1569 -  2.0954  1257   141  0.91  15.64   1.00     0.98       3923.24|
| 13:  2.0954 -  2.0404  1278   141  0.91  15.69   0.98     0.95       3311.20|
| 14:  2.0404 -  1.9907   754    85  0.92  13.43   0.96     0.92       2361.17|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2361.17 max =        10020.00 mean =      6367.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.48|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1572   ksol= 0.32   Bsol= 55.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.57,0.15,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.130594                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1572   ksol= 0.32   Bsol= 55.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-1.57,0.15,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.130594                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7504 0.99   1397  153 0.1016 0.1330       5.428      5.5477|
|  2:  4.7504 -  3.7905 0.99   1340  153 0.0846 0.1129      5.4406       5.645|
|  3:  3.7905 -  3.3173 0.99   1311  146 0.1018 0.1525      5.4521      5.8481|
|  4:  3.3173 -  3.0166 0.99   1308  139 0.1159 0.1531      5.4185      5.5628|
|  5:  3.0166 -  2.8019 0.99   1306  146 0.1267 0.1613      5.2976      5.5274|
|  6:  2.8019 -  2.6377 0.99   1292  148 0.1186 0.1995      5.1966         5.5|
|  7:  2.6377 -  2.5062 0.99   1287  144 0.1221 0.1629      5.1549      5.3272|
|  8:  2.5062 -  2.3976 0.98   1282  138 0.1106 0.1614      5.0584       5.312|
|  9:  2.3976 -  2.3056 0.98   1276  147 0.1144 0.1853      5.0221      5.3215|
| 10:  2.3056 -  2.2263 0.99   1274  139 0.1079 0.1680       4.928      5.1637|
| 11:  2.2263 -  2.1569 0.98   1268  139 0.1083 0.1715      4.9183      5.2026|
| 12:  2.1569 -  2.0954 0.97   1257  141 0.1099 0.1718      4.8629      5.2681|
| 13:  2.0954 -  2.0404 1.00   1278  141 0.1027 0.1736      4.7614      5.0058|
| 14:  2.0404 -  1.9907 0.58    754   85 0.0879 0.1702      4.6037      4.9263|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7504  1397   153  0.93   9.89   0.98     0.94       8078.10|
|  2:  4.7504 -  3.7905  1340   153  0.95   8.02   1.01     0.99       9367.96|
|  3:  3.7905 -  3.3173  1311   146  0.94  10.95   1.02     1.02      10019.79|
|  4:  3.3173 -  3.0166  1308   139  0.92  13.09   1.01     0.99       9764.39|
|  5:  3.0166 -  2.8019  1306   146  0.91  15.36   1.00     0.97       7971.81|
|  6:  2.8019 -  2.6377  1292   148  0.90  16.09   0.98     0.96       7001.08|
|  7:  2.6377 -  2.5062  1287   144  0.91  15.55   0.99     0.96       6212.74|
|  8:  2.5062 -  2.3976  1282   138  0.91  14.89   0.99     0.97       5332.44|
|  9:  2.3976 -  2.3056  1276   147  0.91  15.51   1.00     0.96       5008.41|
| 10:  2.3056 -  2.2263  1274   139  0.90  15.58   1.00     0.96       4221.33|
| 11:  2.2263 -  2.1569  1268   139  0.90  15.93   1.00     0.96       4337.78|
| 12:  2.1569 -  2.0954  1257   141  0.91  15.63   1.01     0.99       3921.66|
| 13:  2.0954 -  2.0404  1278   141  0.91  15.70   0.99     0.97       3312.52|
| 14:  2.0404 -  1.9907   754    85  0.92  13.44   0.97     0.94       2363.81|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2363.81 max =        10019.79 mean =      6366.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.80 mean =        13.93|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.48|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.24   16.34    None  None   None       |
|    all(noH): 2823   0      0.00    83.24   16.34    None  None   None       |
|    Sol.    : 438    0      0.00    80.25   38.88    None  None   None       |
|    Mac.    : 2385   0      0.20    83.24   12.20    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:     0.003 -   8.327:  788   |   5:    41.624 -  49.948:  102        |
|      1:     8.327 -  16.651: 1259   |   6:    49.948 -  58.272:   79        |
|      2:    16.651 -  24.975:  288   |   7:    58.272 -  66.596:   36        |
|      3:    24.975 -  33.299:  127   |   8:    66.596 -  74.920:   18        |
|      4:    33.299 -  41.624:  122   |   9:    74.920 -  83.244:    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)= 274         
Filter by distance & map next to the model:
   mapped sites are within: 0.477 - 4.896
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 267 from: 274
   mapped sites are within: 0.701 - 4.896

peak=    5.532 closest distance to " O   HOH Z 113 " =    2.219
peak=    5.132 closest distance to " CB  GLN A 223 " =    1.470
peak=    4.992 closest distance to " O   HOH Z 142 " =    1.672
peak=    4.957 closest distance to " NE2 GLN A  11 " =    1.122
peak=    4.955 closest distance to " O   HOH Z 126 " =    1.866
peak=    4.913 closest distance to " CG  PRO A  54 " =    1.285
peak=    4.900 closest distance to " CB  ARG A  79 " =    1.364
peak=    4.835 closest distance to " CB  ARG A 275 " =    0.916
peak=    4.775 closest distance to " CB  GLN A 183 " =    1.252
peak=    4.608 closest distance to " CB  ARG A 190 " =    1.705
peak=    4.536 closest distance to " O   HOH Z 298 " =    1.878
peak=    4.494 closest distance to " CZ  PHE A 218 " =    1.068
peak=    4.475 closest distance to " O   HOH Z  78 " =    1.700
peak=    4.473 closest distance to " CB  GLU A 152 " =    1.210
peak=    4.450 closest distance to " O   HOH Z 232 " =    2.410
peak=    4.438 closest distance to " CB  SER A  63 " =    1.160
peak=    4.415 closest distance to " O   HOH Z  15 " =    2.112
peak=    4.361 closest distance to " O   HOH Z 369 " =    2.290
peak=    4.341 closest distance to " O   HOH Z 250 " =    1.481
peak=    4.340 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.327 closest distance to " O   HOH Z  53 " =    2.490
peak=    4.326 closest distance to " O   HOH Z 189 " =    2.919
peak=    4.288 closest distance to " CB  PRO A  54 " =    0.918
peak=    4.259 closest distance to " O   HOH Z 303 " =    2.141
peak=    4.248 closest distance to " CD2 TRP A 179 " =    1.315
peak=    4.215 closest distance to " O   HOH Z 158 " =    3.070
peak=    4.213 closest distance to " CG  PRO A 213 " =    1.161
peak=    4.207 closest distance to " O   HOH Z 423 " =    2.007
peak=    4.201 closest distance to " CE  LYS A  76 " =    0.864
peak=    4.194 closest distance to " O   HOH Z 427 " =    3.009
peak=    4.194 closest distance to " O   HOH Z 287 " =    2.164
peak=    4.181 closest distance to " CB  ASN A 148 " =    1.460
peak=    4.161 closest distance to " O   HOH Z 272 " =    1.873
peak=    4.155 closest distance to " O   HOH Z 392 " =    2.933
peak=    4.154 closest distance to " C   PRO A 198 " =    1.438
peak=    4.112 closest distance to " CA  ASN A 215 " =    1.059
peak=    4.111 closest distance to " O   HOH Z 313 " =    2.069
peak=    4.078 closest distance to " CG  PRO A 198 " =    1.240
peak=    4.059 closest distance to " CG2 VAL A 257 " =    0.833
peak=    4.051 closest distance to " NZ  LYS A 117 " =    3.258
peak=    4.037 closest distance to " ND2 ASN A 187 " =    1.470
peak=    4.027 closest distance to " CB  GLU A 277 " =    3.638
peak=    4.010 closest distance to " O   HOH Z 126 " =    1.988
peak=    4.007 closest distance to " CB  VAL A 265 " =    1.265
peak=    4.006 closest distance to " O   SER A  87 " =    2.255
peak=    4.000 closest distance to " CB  LEU A 228 " =    1.091
peak=    3.981 closest distance to " O   HOH Z 180 " =    2.173
peak=    3.979 closest distance to " O   HOH Z 346 " =    1.745
peak=    3.962 closest distance to " O   HOH Z  61 " =    1.656
peak=    3.918 closest distance to " O   HOH Z 406 " =    1.640
peak=    3.904 closest distance to " CA  ARG A  36 " =    1.055
peak=    3.871 closest distance to " CD  ARG A 159 " =    0.744
peak=    3.859 closest distance to " CB  TRP A 266 " =    1.020
peak=    3.846 closest distance to " O  BHOH Z 338 " =    2.344
peak=    3.843 closest distance to " CB  ASN A  39 " =    0.903
peak=    3.841 closest distance to " OD1 ASN A  69 " =    2.627
peak=    3.839 closest distance to " O   HOH Z  40 " =    1.760
peak=    3.827 closest distance to " NH1AARG A 145 " =    1.295
peak=    3.816 closest distance to " CB  TYR A 169 " =    0.735
peak=    3.811 closest distance to " O   HOH Z 316 " =    3.146
peak=    3.810 closest distance to " CD  LYS A 166 " =    1.267
peak=    3.809 closest distance to " O   HOH Z 403 " =    1.537
peak=    3.807 closest distance to " OG BSER A 164 " =    2.326
peak=    3.801 closest distance to " O   HOH Z 209 " =    2.270
peak=    3.788 closest distance to " O   HOH Z 265 " =    2.157
peak=    3.782 closest distance to " CG  MET A 185 " =    1.137
peak=    3.774 closest distance to " O   ASN A  74 " =    1.433
peak=    3.770 closest distance to " ND2 ASN A 249 " =    0.867
peak=    3.765 closest distance to " CA  ARG A 195 " =    1.238
peak=    3.759 closest distance to " CB  ASP A 140 " =    1.126
peak=    3.759 closest distance to " CB  ASN A 110 " =    1.077
peak=    3.757 closest distance to " O   HOH Z 389 " =    1.824
peak=    3.747 closest distance to " O   HOH Z 234 " =    3.730
peak=    3.739 closest distance to " O   HOH Z 359 " =    1.564
peak=    3.739 closest distance to " CA  THR A 264 " =    0.911
peak=    3.739 closest distance to " O   HOH Z 248 " =    1.615
peak=    3.717 closest distance to " O   HOH Z 193 " =    1.866
peak=    3.705 closest distance to " CB  ASN A 142 " =    1.056
peak=    3.694 closest distance to " O   HOH Z 214 " =    2.198
peak=    3.690 closest distance to " O   HOH Z 245 " =    1.299
peak=    3.679 closest distance to " CA  ALA A  51 " =    0.910
peak=    3.678 closest distance to " O   HOH Z 133 " =    2.712
peak=    3.668 closest distance to " O   HOH Z 368 " =    3.625
peak=    3.666 closest distance to " CB  VAL A 202 " =    1.578
peak=    3.654 closest distance to " CG  LEU A 167 " =    1.275
peak=    3.650 closest distance to " O   HOH Z 185 " =    1.882
peak=    3.647 closest distance to " CG2 ILE A 120 " =    1.095
peak=    3.642 closest distance to " O   HOH Z 421 " =    2.109
peak=    3.640 closest distance to " O   HOH Z 291 " =    1.556
peak=    3.638 closest distance to " CB  THR A  31 " =    1.625
peak=    3.638 closest distance to " CB  GLU A  46 " =    0.979
peak=    3.636 closest distance to " O   HOH Z 337 " =    3.629
peak=    3.623 closest distance to " O   HOH Z   1 " =    1.989
peak=    3.616 closest distance to " O   HOH Z 128 " =    2.088
peak=    3.612 closest distance to " O   HOH Z 172 " =    3.358
peak=    3.605 closest distance to " O   HOH Z  10 " =    1.777
peak=    3.598 closest distance to " O   HOH Z  21 " =    1.831
peak=    3.592 closest distance to " CD  ARG A 269 " =    0.915
peak=    3.582 closest distance to " O   HOH Z 402 " =    1.376
peak=    3.572 closest distance to " O   HOH Z  43 " =    1.911
peak=    3.565 closest distance to " O   HOH Z 280 " =    2.943
peak=    3.561 closest distance to " O   HOH Z 148 " =    3.429
peak=    3.556 closest distance to " O   HOH Z 368 " =    2.177
peak=    3.555 closest distance to " O  BHOH Z  74 " =    1.150
peak=    3.552 closest distance to " CE1 PHE A  38 " =    1.264
peak=    3.540 closest distance to " CD2 LEU A 297 " =    0.819
peak=    3.531 closest distance to " O   HOH Z 419 " =    2.105
peak=    3.522 closest distance to " O   HOH Z  97 " =    2.492
peak=    3.518 closest distance to " CA  TYR A 116 " =    1.338
peak=    3.517 closest distance to " CA  TYR A  30 " =    1.039
peak=    3.517 closest distance to " CG  ARG A  66 " =    2.476
peak=    3.515 closest distance to " O   HOH Z 371 " =    2.993
peak=    3.514 closest distance to " CB  ARG A 139 " =    1.041
peak=    3.511 closest distance to " N   ASN A  39 " =    1.273
peak=    3.509 closest distance to " CD1 LEU A  96 " =    0.702
peak=    3.508 closest distance to " CZ3 TRP A 266 " =    1.114
peak=    3.505 closest distance to " CG2AVAL A  72 " =    1.673
peak=    3.500 closest distance to " CG1 VAL A 153 " =    1.076
peak=    3.499 closest distance to " O   HOH Z 417 " =    3.459
peak=    3.499 closest distance to " O   HOH Z 147 " =    1.865
peak=    3.498 closest distance to " CG  PRO A 243 " =    1.023
peak=    3.494 closest distance to " O   HOH Z 126 " =    1.606
peak=    3.490 closest distance to " O   HOH Z 261 " =    1.881
peak=    3.490 closest distance to " CB  SER A 212 " =    1.131
peak=    3.484 closest distance to " O   HOH Z  59 " =    2.001
peak=    3.482 closest distance to " O   HOH Z 411 " =    3.949
peak=    3.478 closest distance to " N   ARG A 156 " =    1.376
peak=    3.477 closest distance to " CG2 ILE A  20 " =    1.331
peak=    3.475 closest distance to " O   HOH Z 425 " =    2.011
peak=    3.471 closest distance to " CG  GLN A  11 " =    1.695
peak=    3.461 closest distance to " CA  ALA A 158 " =    1.301
peak=    3.451 closest distance to " CG  GLU A  37 " =    0.860
peak=    3.449 closest distance to " O   HOH Z 394 " =    4.046
peak=    3.444 closest distance to " O   HOH Z  88 " =    3.197
peak=    3.443 closest distance to " O   HOH Z  97 " =    1.990
peak=    3.439 closest distance to " NE2 GLN A  73 " =    3.894
peak=    3.438 closest distance to " CG  PRO A  90 " =    1.284
peak=    3.425 closest distance to " NZ  LYS A  48 " =    1.211
peak=    3.424 closest distance to " O   HOH Z 213 " =    1.967
peak=    3.420 closest distance to " O   HOH Z 285 " =    2.380
peak=    3.420 closest distance to " CB  LEU A  83 " =    0.746
peak=    3.419 closest distance to " O   HOH Z 299 " =    4.390
peak=    3.417 closest distance to " CE1 TYR A 186 " =    1.394
peak=    3.416 closest distance to " CA  SER A  87 " =    1.039
peak=    3.415 closest distance to " NE2 HIS A 207 " =    1.226
peak=    3.412 closest distance to " CB  ALA A 291 " =    1.244
peak=    3.406 closest distance to " CZ2 TRP A 179 " =    1.795
peak=    3.405 closest distance to " OG  SER A  22 " =    2.642
peak=    3.403 closest distance to " CB  SER A   3 " =    1.247
peak=    3.401 closest distance to " O   HOH Z 188 " =    1.915
peak=    3.398 closest distance to " CG1 ILE A  33 " =    1.197
peak=    3.394 closest distance to " N   TYR A 116 " =    1.567
peak=    3.383 closest distance to " N   PHE A 130 " =    1.235
peak=    3.382 closest distance to " O   HOH Z 128 " =    2.278
peak=    3.381 closest distance to " O   HOH Z  88 " =    2.557
peak=    3.376 closest distance to " O   HOH Z 353 " =    2.668
peak=    3.375 closest distance to " CB  MET A  47 " =    1.101
peak=    3.372 closest distance to " OG BSER A  99 " =    2.331
peak=    3.365 closest distance to " O   HOH Z 294 " =    1.501
peak=    3.364 closest distance to " CB  TYR A 116 " =    0.750
peak=    3.356 closest distance to " CB  GLU A 128 " =    0.967
peak=    3.356 closest distance to " CD1 LEU A 300 " =    1.219
peak=    3.353 closest distance to " O   HOH Z 407 " =    2.499
peak=    3.339 closest distance to " O   HOH Z 273 " =    2.879
peak=    3.338 closest distance to " O   MET A 105 " =    1.941
peak=    3.336 closest distance to " O   HOH Z 258 " =    2.139
peak=    3.334 closest distance to " O   HOH Z  80 " =    1.622
peak=    3.331 closest distance to " OD2 ASP A 286 " =    3.189
peak=    3.329 closest distance to " CB  TYR A 169 " =    0.795
peak=    3.327 closest distance to " CB  GLN A  88 " =    1.192
peak=    3.322 closest distance to " CA  ALA A 160 " =    0.922
peak=    3.319 closest distance to " CG1 ILE A  49 " =    1.555
peak=    3.317 closest distance to " CG1 VAL A 189 " =    2.068
peak=    3.317 closest distance to " CB  PHE A 204 " =    0.701
peak=    3.314 closest distance to " CA  MET A 105 " =    1.012
peak=    3.306 closest distance to " O   THR A 220 " =    1.295
peak=    3.304 closest distance to " CA  ILE A 234 " =    1.005
peak=    3.303 closest distance to " O   HOH Z 258 " =    1.569
peak=    3.297 closest distance to " CA  ALA A 154 " =    1.002
peak=    3.294 closest distance to " O   HOH Z 365 " =    2.877
peak=    3.292 closest distance to " N   ASN A 127 " =    1.271
peak=    3.290 closest distance to " O   HOH Z 325 " =    2.457
peak=    3.290 closest distance to " CD  LYS A  76 " =    1.927
peak=    3.285 closest distance to " O   HOH Z 171 " =    3.967
peak=    3.284 closest distance to " CB  ASP A 298 " =    1.167
peak=    3.281 closest distance to " CB  PRO A  90 " =    1.152
peak=    3.280 closest distance to " CG2 ILE A 239 " =    0.710
peak=    3.280 closest distance to " CB  ALA A 242 " =    0.927
peak=    3.277 closest distance to " CG2 VAL A 197 " =    1.096
peak=    3.274 closest distance to " O   HOH Z 422 " =    2.707
peak=    3.272 closest distance to " CB  LYS A 117 " =    1.181
peak=    3.271 closest distance to " CA  ALA A 291 " =    0.772
peak=    3.269 closest distance to " O   HOH Z 344 " =    3.235
peak=    3.267 closest distance to " CB  ALA A 248 " =    0.899
peak=    3.265 closest distance to " CA  ASP A 191 " =    1.272
peak=    3.263 closest distance to " CB  TRP A 179 " =    1.396
peak=    3.259 closest distance to " CA  ALA A 233 " =    1.186
peak=    3.257 closest distance to " CB  GLN A  89 " =    1.334
peak=    3.255 closest distance to " O   HOH Z 203 " =    1.661
peak=    3.247 closest distance to " CA  ASP A 162 " =    1.051
peak=    3.247 closest distance to " O   HOH Z 426 " =    1.879
peak=    3.245 closest distance to " O   HOH Z 193 " =    1.711
peak=    3.239 closest distance to " CG  GLN A  88 " =    1.058
peak=    3.235 closest distance to " O   HOH Z 329 " =    4.179
peak=    3.235 closest distance to " O   HOH Z 218 " =    4.705
peak=    3.234 closest distance to " CD  ARG A  66 " =    2.452
peak=    3.234 closest distance to " CA  ASN A 217 " =    1.188
peak=    3.233 closest distance to " CA  ALA A  84 " =    1.300
peak=    3.231 closest distance to " O   HOH Z 371 " =    1.734
peak=    3.230 closest distance to " O   HOH Z 173 " =    1.839
peak=    3.230 closest distance to " NH2BARG A 145 " =    2.092
peak=    3.225 closest distance to " O   ALA A   1 " =    1.636
peak=    3.223 closest distance to " CB  ARG A 138 " =    0.963
peak=    3.222 closest distance to " O   HOH Z 234 " =    1.932
peak=    3.222 closest distance to " N   TYR A 247 " =    1.348
peak=    3.221 closest distance to " O   HOH Z 132 " =    2.655
peak=    3.215 closest distance to " CD1 ILE A 199 " =    1.015
peak=    3.208 closest distance to " CA  VAL A 125 " =    1.109
peak=    3.207 closest distance to " CB  ASN A 215 " =    1.142
peak=    3.206 closest distance to " O   HOH Z 327 " =    1.541
peak=    3.201 closest distance to " CB  ALA A 291 " =    0.787
peak=    3.197 closest distance to " OG1 THR A 294 " =    2.422
peak=    3.196 closest distance to " CB  LYS A 290 " =    1.012
peak=    3.196 closest distance to " CB  ILE A 120 " =    1.270
peak=    3.192 closest distance to " CA  THR A 221 " =    1.037
peak=    3.189 closest distance to " CB  ALA A   9 " =    1.544
peak=    3.186 closest distance to " CE  LYS A  48 " =    1.085
peak=    3.181 closest distance to " CA  ARG A 159 " =    1.228
peak=    3.181 closest distance to " OD2 ASP A 286 " =    2.857
peak=    3.179 closest distance to " CA  ARG A 102 " =    1.071
peak=    3.179 closest distance to " CD BLYS A 290 " =    0.940
peak=    3.179 closest distance to " ND1 HIS A  86 " =    1.747
peak=    3.171 closest distance to " OG1 THR A 264 " =    0.776
peak=    3.170 closest distance to " CG  ARG A 138 " =    1.148
peak=    3.170 closest distance to " O   HOH Z 130 " =    2.223
peak=    3.169 closest distance to " CG2 ILE A 234 " =    0.830
peak=    3.168 closest distance to " O   HOH Z 305 " =    3.560
peak=    3.167 closest distance to " O   HOH Z 214 " =    3.752
peak=    3.165 closest distance to " O   HOH Z  44 " =    2.976
peak=    3.164 closest distance to " CA  ALA A 129 " =    1.272
peak=    3.161 closest distance to " O   HOH Z 410 " =    2.834
peak=    3.160 closest distance to " CG  LYS A  76 " =    0.936
peak=    3.155 closest distance to " O   HOH Z 251 " =    1.613
peak=    3.144 closest distance to " O   HOH Z  62 " =    2.087
peak=    3.141 closest distance to " O   HOH Z  47 " =    1.794
peak=    3.137 closest distance to " CB  ALA A   1 " =    4.896
peak=    3.137 closest distance to " O   HOH Z 287 " =    2.297
peak=    3.135 closest distance to " OE2 GLU A  53 " =    2.012
peak=    3.129 closest distance to " CB  SER A 141 " =    0.992
peak=    3.123 closest distance to " O   HOH Z 116 " =    1.778
peak=    3.123 closest distance to " O   HOH Z 285 " =    1.943
peak=    3.122 closest distance to " NE  ARG A  79 " =    1.015
peak=    3.121 closest distance to " CB  GLN A 205 " =    1.111
peak=    3.117 closest distance to " O   HOH Z 383 " =    2.246
peak=    3.111 closest distance to " O   HOH Z  88 " =    2.627
peak=    3.110 closest distance to " CB  ALA A 114 " =    1.091
peak=    3.092 closest distance to " N   ASP A 162 " =    1.169
peak=    3.086 closest distance to " CD  LYS A 119 " =    1.390
peak=    3.086 closest distance to " O   HOH Z 336 " =    1.658
peak=    3.081 closest distance to " O   SER A 164 " =    1.273
peak=    3.075 closest distance to " O   HOH Z 409 " =    3.025
peak=    3.072 closest distance to " O   HOH Z 332 " =    1.507
peak=    3.065 closest distance to " CB  ALA A 227 " =    1.065
peak=    3.057 closest distance to " CA  ASP A 140 " =    1.201
peak=    3.053 closest distance to " CA  SER A  32 " =    1.624
peak=    3.043 closest distance to " O   HOH Z 361 " =    3.184
peak=    3.037 closest distance to " ND2 ASN A 110 " =    1.562

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.984 - 5.769
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 190
   mapped sites are within: 0.984 - 5.769

peak=   -4.788 closest distance to " CD  ARG A  14 " =    3.493
peak=   -4.735 closest distance to " CD  GLN A  58 " =    0.984
peak=   -4.475 closest distance to " CG1 VAL A 112 " =    2.647
peak=   -4.423 closest distance to " O   HOH Z 377 " =    2.187
peak=   -4.420 closest distance to " CD  ARG A 156 " =    2.139
peak=   -4.419 closest distance to " CB  PRO A 243 " =    2.680
peak=   -4.376 closest distance to " C   HIS A 108 " =    1.104
peak=   -4.348 closest distance to " O   VAL A  67 " =    2.730
peak=   -4.264 closest distance to " O   HOH Z 231 " =    2.251
peak=   -4.263 closest distance to " CZ3 TRP A 179 " =    1.181
peak=   -4.220 closest distance to " O   HOH Z 266 " =    5.450
peak=   -4.144 closest distance to " CG1 VAL A 112 " =    2.881
peak=   -4.132 closest distance to " O   PRO A 198 " =    1.305
peak=   -4.102 closest distance to " N   ALA A  43 " =    2.625
peak=   -4.088 closest distance to " CD2 PHE A 192 " =    2.027
peak=   -4.087 closest distance to " OG BSER A 134 " =    1.318
peak=   -4.048 closest distance to " CA  VAL A  67 " =    2.947
peak=   -4.047 closest distance to " O   HOH Z  73 " =    2.388
peak=   -4.040 closest distance to " CG  GLN A 223 " =    2.180
peak=   -4.014 closest distance to " CE  MET A 105 " =    2.482
peak=   -3.991 closest distance to " OXT GLY A 302 " =    2.806
peak=   -3.987 closest distance to " O   HOH Z 198 " =    1.859
peak=   -3.913 closest distance to " CD2 TYR A 293 " =    2.000
peak=   -3.907 closest distance to " O   HOH Z 372 " =    2.293
peak=   -3.883 closest distance to " O   HOH Z 196 " =    1.998
peak=   -3.872 closest distance to " CE BMET A  47 " =    1.436
peak=   -3.839 closest distance to " CB  ALA A 291 " =    2.293
peak=   -3.824 closest distance to " CB  ALA A  43 " =    2.523
peak=   -3.806 closest distance to " O   HOH Z 185 " =    2.336
peak=   -3.802 closest distance to " OG  SER A  97 " =    2.259
peak=   -3.799 closest distance to " OD1 ASP A 171 " =    1.653
peak=   -3.791 closest distance to " CE2 TYR A  30 " =    2.736
peak=   -3.791 closest distance to " O   ILE A 109 " =    2.574
peak=   -3.783 closest distance to " CA  ASP A 298 " =    1.108
peak=   -3.772 closest distance to " O   HOH Z 389 " =    1.969
peak=   -3.770 closest distance to " ND2 ASN A  45 " =    1.734
peak=   -3.765 closest distance to " O   HOH Z  10 " =    1.475
peak=   -3.721 closest distance to " O   HOH Z 290 " =    1.341
peak=   -3.709 closest distance to " O   HOH Z 114 " =    3.127
peak=   -3.698 closest distance to " CD1 PHE A  59 " =    2.054
peak=   -3.694 closest distance to " CD1 LEU A 101 " =    2.353
peak=   -3.670 closest distance to " NH2AARG A 275 " =    5.324
peak=   -3.666 closest distance to " OD1 ASN A 148 " =    1.506
peak=   -3.657 closest distance to " O   HOH Z 407 " =    3.020
peak=   -3.652 closest distance to " N   ALA A 248 " =    1.605
peak=   -3.652 closest distance to " CE2 PHE A  61 " =    2.634
peak=   -3.649 closest distance to " NE2 GLN A 194 " =    1.886
peak=   -3.646 closest distance to " CA  GLY A 203 " =    2.362
peak=   -3.645 closest distance to " CB  ASN A  39 " =    2.343
peak=   -3.643 closest distance to " O   HOH Z 394 " =    1.501
peak=   -3.640 closest distance to " ND2 ASN A  45 " =    1.161
peak=   -3.639 closest distance to " ND2 ASN A 249 " =    2.387
peak=   -3.638 closest distance to " CG  PHE A 283 " =    2.732
peak=   -3.637 closest distance to " O   SER A 210 " =    2.010
peak=   -3.637 closest distance to " CB  TRP A  85 " =    2.523
peak=   -3.635 closest distance to " CG2 THR A 178 " =    2.346
peak=   -3.619 closest distance to " CG2 ILE A  49 " =    2.721
peak=   -3.612 closest distance to " O   HOH Z 351 " =    1.515
peak=   -3.591 closest distance to " CG  ARG A  66 " =    2.351
peak=   -3.591 closest distance to " O   HOH Z 313 " =    1.908
peak=   -3.585 closest distance to " CD1 LEU A 255 " =    2.847
peak=   -3.579 closest distance to " CG2 ILE A 263 " =    2.286
peak=   -3.568 closest distance to " CG  ASP A 132 " =    2.319
peak=   -3.555 closest distance to " O   PRO A 163 " =    2.080
peak=   -3.550 closest distance to " CG1 VAL A 250 " =    2.675
peak=   -3.543 closest distance to " NE2 GLN A  88 " =    1.843
peak=   -3.526 closest distance to " CZ  TYR A 169 " =    1.763
peak=   -3.522 closest distance to " CB  ALA A 248 " =    2.332
peak=   -3.514 closest distance to " O   HOH Z 211 " =    1.571
peak=   -3.514 closest distance to " O   HOH Z  51 " =    1.735
peak=   -3.512 closest distance to " O   HOH Z 357 " =    2.049
peak=   -3.511 closest distance to " O   ALA A  10 " =    1.702
peak=   -3.502 closest distance to " CA  GLY A 241 " =    3.211
peak=   -3.502 closest distance to " CG  ARG A 269 " =    2.359
peak=   -3.498 closest distance to " CB  ALA A 291 " =    2.318
peak=   -3.485 closest distance to " OD2 ASP A 191 " =    1.460
peak=   -3.483 closest distance to " O   HOH Z 174 " =    2.615
peak=   -3.473 closest distance to " CD  ARG A 139 " =    1.618
peak=   -3.472 closest distance to " C   LEU A 143 " =    1.082
peak=   -3.467 closest distance to " O   HOH Z  71 " =    2.165
peak=   -3.432 closest distance to " CZ  PHE A 155 " =    1.270
peak=   -3.432 closest distance to " O   HOH Z  38 " =    1.604
peak=   -3.428 closest distance to " NE2 GLN A 278 " =    1.771
peak=   -3.426 closest distance to " O   HOH Z  37 " =    1.792
peak=   -3.423 closest distance to " O   HOH Z 166 " =    1.974
peak=   -3.410 closest distance to " NE2 GLN A  11 " =    1.754
peak=   -3.404 closest distance to " O   HOH Z 102 " =    1.592
peak=   -3.404 closest distance to " O   HOH Z 429 " =    2.130
peak=   -3.402 closest distance to " CG  GLU A 277 " =    1.196
peak=   -3.400 closest distance to " CB  ASP A 286 " =    2.076
peak=   -3.397 closest distance to " CB  ALA A 129 " =    2.422
peak=   -3.397 closest distance to " O   HOH Z   6 " =    1.430
peak=   -3.392 closest distance to " O   VAL A 189 " =    2.716
peak=   -3.392 closest distance to " CG  HIS A  86 " =    1.101
peak=   -3.383 closest distance to " O   HOH Z 298 " =    1.251
peak=   -3.378 closest distance to " O   HOH Z 348 " =    2.229
peak=   -3.366 closest distance to " ND2 ASN A 187 " =    1.512
peak=   -3.353 closest distance to " CD  GLN A 223 " =    1.382
peak=   -3.353 closest distance to " ND2 ASN A  60 " =    1.301
peak=   -3.352 closest distance to " CG1 VAL A 125 " =    1.854
peak=   -3.351 closest distance to " NH2 ARG A  79 " =    1.561
peak=   -3.346 closest distance to " O   PHE A 218 " =    1.535
peak=   -3.343 closest distance to " O   HOH Z  60 " =    1.819
peak=   -3.341 closest distance to " CG  LEU A  83 " =    1.960
peak=   -3.340 closest distance to " CD2 TYR A 247 " =    2.409
peak=   -3.335 closest distance to " OE1 GLN A  88 " =    1.089
peak=   -3.334 closest distance to " CE3 TRP A 150 " =    2.273
peak=   -3.331 closest distance to " O   SER A 135 " =    1.433
peak=   -3.331 closest distance to " CD2 PHE A  61 " =    2.086
peak=   -3.329 closest distance to " C   PRO A  90 " =    1.538
peak=   -3.325 closest distance to " O   HOH Z 311 " =    3.804
peak=   -3.320 closest distance to " OE2 GLU A 152 " =    1.275
peak=   -3.318 closest distance to " CD1 ILE A 199 " =    2.495
peak=   -3.317 closest distance to " O   VAL A 174 " =    2.105
peak=   -3.316 closest distance to " O   HOH Z  13 " =    1.652
peak=   -3.308 closest distance to " O   HOH Z 134 " =    3.266
peak=   -3.305 closest distance to " CD  GLN A 223 " =    1.005
peak=   -3.289 closest distance to " CG2 VAL A 189 " =    2.132
peak=   -3.285 closest distance to " CA  GLY A 241 " =    2.339
peak=   -3.284 closest distance to " O   HOH Z 253 " =    3.922
peak=   -3.276 closest distance to " OD1 ASN A 187 " =    1.643
peak=   -3.272 closest distance to " CA  PRO A 243 " =    2.384
peak=   -3.270 closest distance to " O   VAL A 189 " =    1.636
peak=   -3.259 closest distance to " OH  TYR A 247 " =    2.085
peak=   -3.258 closest distance to " O   HOH Z 426 " =    1.580
peak=   -3.257 closest distance to " O   HOH Z 295 " =    1.547
peak=   -3.257 closest distance to " CE3 TRP A 274 " =    2.411
peak=   -3.253 closest distance to " NE2 GLN A  88 " =    1.184
peak=   -3.243 closest distance to " CG  PRO A 243 " =    1.818
peak=   -3.243 closest distance to " CZ  PHE A 192 " =    2.893
peak=   -3.241 closest distance to " O   SER A  95 " =    1.616
peak=   -3.231 closest distance to " CG1BVAL A  41 " =    2.772
peak=   -3.226 closest distance to " CA  SER A 135 " =    1.318
peak=   -3.225 closest distance to " CZ  PHE A  59 " =    1.579
peak=   -3.224 closest distance to " O   HOH Z 421 " =    3.185
peak=   -3.221 closest distance to " O   TRP A  70 " =    1.456
peak=   -3.220 closest distance to " O   HOH Z 216 " =    1.468
peak=   -3.220 closest distance to " N   THR A  52 " =    1.662
peak=   -3.219 closest distance to " C   MET A 188 " =    1.334
peak=   -3.215 closest distance to " O   ALA A 161 " =    1.753
peak=   -3.215 closest distance to " CG1AVAL A  41 " =    2.726
peak=   -3.212 closest distance to " CE2 PHE A 218 " =    2.440
peak=   -3.212 closest distance to " O   HOH Z  11 " =    1.673
peak=   -3.205 closest distance to " CD  PRO A 213 " =    2.214
peak=   -3.202 closest distance to " O   HOH Z  52 " =    1.522
peak=   -3.200 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.200 closest distance to " CB  PRO A 163 " =    2.457
peak=   -3.196 closest distance to " OG BSER A 134 " =    1.801
peak=   -3.190 closest distance to " CA  GLY A 133 " =    2.068
peak=   -3.189 closest distance to " O   HOH Z 126 " =    1.926
peak=   -3.184 closest distance to " CA  GLY A 241 " =    2.876
peak=   -3.183 closest distance to " C   ASP A 272 " =    2.345
peak=   -3.180 closest distance to " CG1BVAL A  72 " =    2.391
peak=   -3.173 closest distance to " O   ILE A 106 " =    1.952
peak=   -3.173 closest distance to " OD1AASN A 224 " =    1.734
peak=   -3.171 closest distance to " O   HOH Z 171 " =    1.936
peak=   -3.170 closest distance to " O   HOH Z 232 " =    1.484
peak=   -3.170 closest distance to " O   GLN A 240 " =    2.092
peak=   -3.163 closest distance to " O   HOH Z 353 " =    2.240
peak=   -3.163 closest distance to " SG BCYS A 201 " =    1.946
peak=   -3.161 closest distance to " O   HOH Z 191 " =    5.769
peak=   -3.161 closest distance to " O   HOH Z  43 " =    1.690
peak=   -3.160 closest distance to " NH2BARG A 275 " =    1.992
peak=   -3.156 closest distance to " CD  PRO A  90 " =    1.884
peak=   -3.148 closest distance to " NE2 GLN A 223 " =    1.970
peak=   -3.147 closest distance to " O   HOH Z 265 " =    2.349
peak=   -3.146 closest distance to " O   HOH Z 405 " =    2.616
peak=   -3.145 closest distance to " CB  ALA A 100 " =    2.139
peak=   -3.140 closest distance to " O   HOH Z 200 " =    3.234
peak=   -3.136 closest distance to " O   ARG A  24 " =    1.711
peak=   -3.135 closest distance to " CB  ALA A  10 " =    2.278
peak=   -3.134 closest distance to " CG1 VAL A 125 " =    2.374
peak=   -3.129 closest distance to " O   HOH Z 278 " =    1.655
peak=   -3.125 closest distance to " O   HOH Z 139 " =    5.224
peak=   -3.119 closest distance to " O   GLN A 240 " =    2.480
peak=   -3.119 closest distance to " O   TYR A 247 " =    2.885
peak=   -3.118 closest distance to " O   HOH Z 128 " =    2.671
peak=   -3.112 closest distance to " CG1 VAL A 197 " =    2.302
peak=   -3.110 closest distance to " CG1 VAL A  67 " =    3.054
peak=   -3.108 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.107 closest distance to " O   GLY A  80 " =    2.554
peak=   -3.105 closest distance to " O   HOH Z  55 " =    1.240
peak=   -3.101 closest distance to " O   HOH Z 244 " =    1.998
peak=   -3.100 closest distance to " O   ALA A  51 " =    1.272
peak=   -3.086 closest distance to " CD1 LEU A   5 " =    2.538
peak=   -3.080 closest distance to " O   HOH Z 283 " =    5.703
peak=   -3.077 closest distance to " CZ  PHE A  38 " =    1.987
peak=   -3.071 closest distance to " CB  ALA A 114 " =    2.564
peak=   -3.070 closest distance to " CA  HIS A  86 " =    2.392
peak=   -3.057 closest distance to " CD1 TRP A  70 " =    1.087

================= 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    :  0.3292 0.3234   6.073253e+00   6.049834e+00
   1_bss:  0.3099 0.3065   6.040525e+00   6.015571e+00
   1_xyz:  0.2108 0.2345   5.662790e+00   5.741326e+00
   1_adp:  0.1975 0.2358   5.618516e+00   5.751348e+00
   1_occ:  0.1970 0.2356   5.617682e+00   5.752177e+00
   2_bss:  0.1937 0.2334   5.605874e+00   5.743680e+00
   2_xyz:  0.1337 0.1700   5.270623e+00   5.458787e+00
   2_adp:  0.1227 0.1683   5.216508e+00   5.442389e+00
   2_occ:  0.1226 0.1681   5.216282e+00   5.442290e+00
   3_bss:  0.1222 0.1674   5.211971e+00   5.436418e+00
   3_xyz:  0.1183 0.1621   5.185454e+00   5.409256e+00
   3_adp:  0.1178 0.1604   5.178760e+00   5.399393e+00
   3_occ:  0.1177 0.1603   5.178655e+00   5.399624e+00
   4_bss:  0.1175 0.1602   5.178435e+00   5.399832e+00
   4_xyz:  0.1107 0.1572   5.139837e+00   5.382954e+00
   4_adp:  0.1112 0.1563   5.138534e+00   5.376884e+00
   4_occ:  0.1111 0.1562   5.138064e+00   5.376890e+00
   5_bss:  0.1110 0.1562   5.138063e+00   5.376929e+00
   5_xyz:  0.1093 0.1563   5.131179e+00   5.378055e+00
   5_adp:  0.1082 0.1573   5.130489e+00   5.385805e+00
   5_occ:  0.1081 0.1573   5.130504e+00   5.385983e+00
   5_bss:  0.1080 0.1572   5.130594e+00   5.386037e+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:  0.317  49.300  -3.125  -3.071   4.597  -0.000   0.000   0.000
   1_xyz:  0.317  49.300  -3.125  -3.071   4.597  -0.000   0.000   0.000
   1_adp:  0.317  49.300  -3.125  -3.071   4.597  -0.000   0.000   0.000
   1_occ:  0.317  49.300  -3.125  -3.071   4.597  -0.000   0.000   0.000
   2_bss:  0.329  60.595  -3.070  -2.568   0.942  -0.000   0.000   0.000
   2_xyz:  0.329  60.595  -3.070  -2.568   0.942  -0.000   0.000   0.000
   2_adp:  0.329  60.595  -3.070  -2.568   0.942  -0.000   0.000   0.000
   2_occ:  0.329  60.595  -3.070  -2.568   0.942  -0.000   0.000   0.000
   3_bss:  0.331  64.147  -2.684  -2.174   0.119  -0.000   0.000   0.000
   3_xyz:  0.331  64.147  -2.684  -2.174   0.119  -0.000   0.000   0.000
   3_adp:  0.331  64.147  -2.684  -2.174   0.119  -0.000   0.000   0.000
   3_occ:  0.331  64.147  -2.684  -2.174   0.119  -0.000   0.000   0.000
   4_bss:  0.327  58.496  -2.436  -1.941  -0.045  -0.000  -0.000  -0.000
   4_xyz:  0.327  58.496  -2.436  -1.941  -0.045  -0.000  -0.000  -0.000
   4_adp:  0.327  58.496  -2.436  -1.941  -0.045  -0.000  -0.000  -0.000
   4_occ:  0.327  58.496  -2.436  -1.941  -0.045  -0.000  -0.000  -0.000
   5_bss:  0.327  58.496  -2.309  -1.827  -0.062  -0.000  -0.000  -0.000
   5_xyz:  0.327  58.496  -2.309  -1.827  -0.062  -0.000  -0.000  -0.000
   5_adp:  0.327  58.496  -2.309  -1.827  -0.062  -0.000  -0.000  -0.000
   5_occ:  0.327  58.496  -2.309  -1.827  -0.062  -0.000  -0.000  -0.000
   5_bss:  0.320  55.719  -2.039  -1.568   0.154  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  34.119 0.7148  0.8762    30761.328
   1_bss:  32.573 0.7308  0.8799    27244.012
   1_xyz:  22.578 0.8376  0.9766    13942.291
   1_adp:  22.929 0.8337  0.9661    14268.108
   1_occ:  22.970 0.8332  0.9656    14284.837
   2_bss:  22.405 0.8393  0.9397    13952.763
   2_xyz:  15.826 0.8994  0.9748     7481.025
   2_adp:  15.355 0.9034  0.9691     7175.468
   2_occ:  15.350 0.9034  0.9690     7171.402
   3_bss:  15.216 0.9046  0.9694     7078.874
   3_xyz:  14.456 0.9115  0.9708     6658.389
   3_adp:  14.220 0.9136  0.9648     6556.189
   3_occ:  14.228 0.9135  0.9646     6558.556
   4_bss:  14.226 0.9135  0.9683     6560.176
   4_xyz:  13.931 0.9156  0.9720     6341.704
   4_adp:  13.777 0.9170  0.9680     6277.295
   4_occ:  13.777 0.9169  0.9680     6273.207
   5_bss:  13.777 0.9170  0.9706     6274.614
   5_xyz:  13.751 0.9173  0.9701     6317.732
   5_adp:  13.885 0.9163  0.9620     6366.419
   5_occ:  13.886 0.9163  0.9619     6366.954
   5_bss:  13.890 0.9162  0.9704     6366.612
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6834e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6834e-01
   1_xyz:   1.109  0.008  0.072 15.029  0.004  4.111   6.9680e-02
   1_adp:   1.109  0.008  0.072 15.029  0.004  4.111   6.9680e-02
   1_occ:   1.109  0.008  0.072 15.029  0.004  4.111   6.9680e-02
   2_bss:   1.109  0.008  0.072 15.029  0.004  4.111   6.9680e-02
   2_xyz:   1.088  0.009  0.079 15.133  0.004  4.126   6.9388e-02
   2_adp:   1.088  0.009  0.079 15.133  0.004  4.126   6.9388e-02
   2_occ:   1.088  0.009  0.079 15.133  0.004  4.126   6.9388e-02
   3_bss:   1.088  0.009  0.079 15.133  0.004  4.126   6.9388e-02
   3_xyz:   0.921  0.007  0.072 14.526  0.004  4.129   5.2008e-02
   3_adp:   0.921  0.007  0.072 14.526  0.004  4.129   5.2008e-02
   3_occ:   0.921  0.007  0.072 14.526  0.004  4.129   5.2008e-02
   4_bss:   0.921  0.007  0.072 14.526  0.004  4.129   5.2008e-02
   4_xyz:   1.075  0.010  0.083 14.771  0.004  4.115   7.0574e-02
   4_adp:   1.075  0.010  0.083 14.771  0.004  4.115   7.0574e-02
   4_occ:   1.075  0.010  0.083 14.771  0.004  4.115   7.0574e-02
   5_bss:   1.075  0.010  0.083 14.771  0.004  4.115   7.0574e-02
   5_xyz:   1.098  0.010  0.085 14.797  0.004  4.117   7.4272e-02
   5_adp:   1.098  0.010  0.085 14.797  0.004  4.117   7.4272e-02
   5_occ:   1.098  0.010  0.085 14.797  0.004  4.117   7.4272e-02
   5_bss:   1.098  0.010  0.085 14.797  0.004  4.117   7.4272e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.597   2.4260e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.597   2.4260e-01
   1_xyz:   8.289  0.046  0.295 82.875  0.029  2.188   7.3501e-02
   1_adp:   8.289  0.046  0.295 82.875  0.029  2.188   7.3501e-02
   1_occ:   8.289  0.046  0.295 82.875  0.029  2.188   7.3501e-02
   2_bss:   8.289  0.046  0.295 82.875  0.029  2.188   7.3501e-02
   2_xyz:   7.145  0.053  0.283 84.661  0.037  2.296   6.1907e-02
   2_adp:   7.145  0.053  0.283 84.661  0.037  2.296   6.1907e-02
   2_occ:   7.145  0.053  0.283 84.661  0.037  2.296   6.1907e-02
   3_bss:   7.145  0.053  0.283 84.661  0.037  2.296   6.1907e-02
   3_xyz:   6.234  0.044  0.221 81.732  0.036  2.422   3.6554e-02
   3_adp:   6.234  0.044  0.221 81.732  0.036  2.422   3.6554e-02
   3_occ:   6.234  0.044  0.221 81.732  0.036  2.422   3.6554e-02
   4_bss:   6.234  0.044  0.221 81.732  0.036  2.422   3.6554e-02
   4_xyz:   7.266  0.056  0.289 82.961  0.035  2.297   5.2530e-02
   4_adp:   7.266  0.056  0.289 82.961  0.035  2.297   5.2530e-02
   4_occ:   7.266  0.056  0.289 82.961  0.035  2.297   5.2530e-02
   5_bss:   7.266  0.056  0.289 82.961  0.035  2.297   5.2530e-02
   5_xyz:   7.302  0.059  0.286 83.077  0.038  2.287   5.8386e-02
   5_adp:   7.302  0.059  0.286 83.077  0.038  2.287   5.8386e-02
   5_occ:   7.302  0.059  0.286 83.077  0.038  2.287   5.8386e-02
   5_bss:   7.302  0.059  0.286 83.077  0.038  2.287   5.8386e-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:  89.29   0.00  16.28  89.29   0.00  12.45  62.78   4.14  37.12
   1_occ:  89.29   0.00  16.28  89.29   0.00  12.45  62.78   4.14  37.12
   2_bss:  89.29   0.00  16.28  89.29   0.00  12.45  62.78   4.14  37.12
   2_xyz:  89.29   0.00  16.28  89.29   0.00  12.45  62.78   4.14  37.12
   2_adp:  81.10   0.00  17.15  81.10   0.00  12.78  80.84   5.74  40.98
   2_occ:  81.10   0.00  17.15  81.10   0.00  12.78  80.84   5.74  40.98
   3_bss:  81.10   0.00  17.15  81.10   0.00  12.78  80.84   5.74  40.98
   3_xyz:  81.10   0.00  17.15  81.10   0.00  12.78  80.84   5.74  40.98
   3_adp:  80.93   0.81  16.60  80.93   0.81  12.51  80.73   3.19  38.90
   3_occ:  80.93   0.81  16.60  80.93   0.81  12.51  80.73   3.19  38.90
   4_bss:  80.93   0.81  16.60  80.93   0.81  12.51  80.73   3.19  38.90
   4_xyz:  80.93   0.81  16.60  80.93   0.81  12.51  80.73   3.19  38.90
   4_adp:  79.08   0.00  16.19  79.08   1.48  12.28  78.62   0.00  37.48
   4_occ:  79.08   0.00  16.19  79.08   1.48  12.28  78.62   0.00  37.48
   5_bss:  79.08   0.00  16.19  79.08   1.48  12.28  78.62   0.00  37.48
   5_xyz:  79.08   0.00  16.19  79.08   1.48  12.28  78.62   0.00  37.48
   5_adp:  83.24   0.00  16.34  83.24   0.20  12.20  80.25   0.00  38.88
   5_occ:  83.24   0.00  16.34  83.24   0.20  12.20  80.25   0.00  38.88
   5_bss:  83.24   0.00  16.34  83.24   0.20  12.20  80.25   0.00  38.88
------------------------------------------------------------------------
 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:    1.401    0.011    0.262
   1_adp:    1.401    0.011    0.262
   1_occ:    1.401    0.011    0.262
   2_bss:    1.401    0.011    0.262
   2_xyz:    1.055    0.013    0.374
   2_adp:    1.055    0.013    0.374
   2_occ:    1.055    0.013    0.374
   3_bss:    1.055    0.013    0.374
   3_xyz:    1.018    0.013    0.387
   3_adp:    1.018    0.013    0.387
   3_occ:    1.018    0.013    0.387
   4_bss:    1.018    0.013    0.387
   4_xyz:    1.188    0.021    0.404
   4_adp:    1.188    0.021    0.404
   4_occ:    1.188    0.021    0.404
   5_bss:    1.188    0.021    0.404
   5_xyz:    1.478    0.013    0.412
   5_adp:    1.478    0.013    0.412
   5_occ:    1.478    0.013    0.412
   5_bss:    1.478    0.013    0.412
------------------------------------------------------------------------

CPU time actual refinement: 325.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_548/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_548/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_548/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_548/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_548/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.65 
  Macro-tasks:
    bulk solvent and scale       = 36.76  
    individual site refinement   = 140.80 
    weights calculation          = 28.13  
    collect and process          = 6.48   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 212.26 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 103.47 
    alpha_beta                      = 8.20   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 114.84 
    fmodel                         = 6.44   
    r_factors                      = 0.19   
    phase_errors                   = 11.21  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 246.94 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.519 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    669 calls, 103.01 s
gradients_fft:          614 calls, 100.32 s

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

# Date 2008-01-16 Time 05:05:46 PST -0800 (1200488746.09 s)
Start R-work = 0.3292, R-free = 0.3234 (no bulk solvent and anisotropic scale)
Final R-work = 0.1296, R-free = 0.1745 (no bulk solvent and anisotropic scale)

Start R-work = 0.3099, R-free = 0.3065
Final R-work = 0.1080, R-free = 0.1572