# Date 2008-01-16 Time 04:39:43 PST -0800 (1200487183.75 s)
#phil __OFF__

Command line arguments: "../412.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9349
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 412

-------------------------------------------------------------------------------
  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: (69.5475, 46.6953, 86.39, 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: (69.5475, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.98057
Completeness in resolution range: 0.972448
Completeness with d_max=infinity: 0.969369

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8842
                             d_min =   1.9806

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: (69.5475, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.98057
Completeness in resolution range: 0.972448
Completeness with d_max=infinity: 0.969369

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8847 -  4.2373 [2118/2142]  1904   214  10.1%
  bin  2:  4.2373 -  3.3762 [2036/2055]  1835   201   9.9%
  bin  3:  3.3762 -  2.9532 [2008/2027]  1809   199   9.9%
  bin  4:  2.9532 -  2.6849 [1982/2012]  1777   205  10.3%
  bin  5:  2.6849 -  2.4934 [1982/2001]  1786   196   9.9%
  bin  6:  2.4934 -  2.3470 [1965/1990]  1771   194   9.9%
  bin  7:  2.3470 -  2.2299 [1952/1980]  1757   195  10.0%
  bin  8:  2.2299 -  2.1331 [1946/1982]  1751   195  10.0%
  bin  9:  2.1331 -  2.0512 [1931/1973]  1737   194  10.0%
  bin 10:  2.0512 -  1.9806 [1669/1982]  1503   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_412/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: 0.13 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:
        1.81 -     2.42: 19
        2.42 -     3.04: 2224
        3.04 -     3.66: 4715
        3.66 -     4.28: 9126
        4.28 -     4.90: 12420
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.023 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.099 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.123 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  2.152 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28499 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_412/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_412/model_refine_001.geo

CPU time processing inputs: 9.23


============================ 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 = 69.5475 46.69535 86.39 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: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2464   r_free= 0.2449   ksol= 0.00   Bsol= 0.00   scale= 1.007    |
|                                                                             |
| 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:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.795057                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7257 0.99   1380  153 0.2553 0.2487      6.2643      6.2313|
|  2:  4.7257 -  3.7710 0.99   1312  149 0.1877 0.1873      6.1443      6.1561|
|  3:  3.7710 -  3.3003 0.99   1305  145 0.2035 0.2085      6.0528      6.1415|
|  4:  3.3003 -  3.0012 0.99   1290  136 0.2160 0.2386      5.9433      6.0308|
|  5:  3.0012 -  2.7876 0.99   1269  144 0.2381 0.2209      5.8184      5.7415|
|  6:  2.7876 -  2.6242 0.99   1275  145 0.2447 0.2518      5.7799       5.707|
|  7:  2.6242 -  2.4934 0.99   1280  143 0.2521 0.2343      5.7194      5.6389|
|  8:  2.4934 -  2.3853 0.98   1263  135 0.2613 0.2574      5.7156      5.7522|
|  9:  2.3853 -  2.2938 0.98   1251  143 0.2615 0.2643      5.6696      5.6357|
| 10:  2.2938 -  2.2149 0.99   1264  136 0.2676 0.2519      5.6623      5.5829|
| 11:  2.2149 -  2.1459 0.98   1262  142 0.2732 0.2628      5.6143       5.631|
| 12:  2.1459 -  2.0847 0.97   1226  139 0.2845 0.2585      5.6065      5.6299|
| 13:  2.0847 -  2.0300 1.00   1264  137 0.2811 0.2778      5.5066       5.464|
| 14:  2.0300 -  1.9806 0.78    989  112 0.2937 0.2658       5.494      5.3408|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.7257  1380   153  0.81  24.11   0.88     0.82      36784.50|
|  2:  4.7257 -  3.7710  1312   149  0.88  17.54   1.00     0.95      30555.13|
|  3:  3.7710 -  3.3003  1305   145  0.87  18.92   1.03     1.01      25051.74|
|  4:  3.3003 -  3.0012  1290   136  0.87  19.42   1.03     1.01      20343.07|
|  5:  3.0012 -  2.7876  1269   144  0.84  22.47   1.04     1.00      16337.76|
|  6:  2.7876 -  2.6242  1275   145  0.85  22.02   1.03     1.01      13618.52|
|  7:  2.6242 -  2.4934  1280   143  0.84  23.11   1.05     1.02      12501.53|
|  8:  2.4934 -  2.3853  1263   135  0.83  23.35   1.06     1.03      11863.82|
|  9:  2.3853 -  2.2938  1251   143  0.84  23.66   1.08     1.04      11400.97|
| 10:  2.2938 -  2.2149  1264   136  0.82  24.75   1.10     1.05      10830.58|
| 11:  2.2149 -  2.1459  1262   142  0.82  25.09   1.09     1.06      10671.37|
| 12:  2.1459 -  2.0847  1226   139  0.82  25.40   1.11     1.07      10053.77|
| 13:  2.0847 -  2.0300  1264   137  0.81  26.32   1.10     1.05       8676.64|
| 14:  2.0300 -  1.9806   989   112  0.83  24.64   1.10     1.01       6437.40|
|alpha:            min =        0.82 max =            1.07 mean =         1.01|
|beta:             min =     6437.40 max =        36784.50 mean =     16446.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.98 mean =        22.86|
|phase err.(test): min =        0.00 max =           89.09 mean =        22.65|
|-----------------------------------------------------------------------------|

============================== 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 = 3.449570              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.217   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.353952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.789   (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 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      211 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2013 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1845 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2870 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4688 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4438 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5666 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6754 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.180 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.716)------------------------------------------|
|    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: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2464   r_free= 0.2449   ksol= 0.00   Bsol= 0.00   scale= 1.007    |
|                                                                             |
| 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:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.795057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2291   r_free= 0.2252   ksol= 0.32   Bsol= 35.37   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.89,-1.64,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.755732                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.125316              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.201   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.193548              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.665   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2291      final r-factor (work) = 0.1338          |
| start r-factor (free) = 0.2252      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2387 = 3.13 * 0.50 * 5.8087 + 1.00 * 0.1616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5475 = 3.13 * 0.50 * 5.4313 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1338      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0572 = 0.19 * 1.00 * 5.4313 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0068 = 0.19 * 1.00 * 5.1664 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.716)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    65.93   16.69    None  None   None       |
|    all(noH): 2823   0      1.01    65.93   16.69    None  None   None       |
|    Sol.    : 438    0      7.14    65.93   37.26    None  None   None       |
|    Mac.    : 2385   0      1.01    63.44   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.008 -   7.501:  334   |   5:    33.469 -  39.962:  108        |
|      1:     7.501 -  13.993: 1398   |   6:    39.962 -  46.454:  100        |
|      2:    13.993 -  20.485:  490   |   7:    46.454 -  52.946:   84        |
|      3:    20.485 -  26.977:  147   |   8:    52.946 -  59.438:   45        |
|      4:    26.977 -  33.469:  108   |   9:    59.438 -  65.930:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1570             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1214 r_free = 0.1567             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1567   ksol= 0.32   Bsol= 35.37   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.89,-1.64,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.174170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1557   ksol= 0.31   Bsol= 38.49   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.57,-1.66,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.172829                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.468219              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.373  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.114888              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.779  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1497          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8573 = 1.47 * 0.50 * 5.1723 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8246 = 1.47 * 0.50 * 5.1373 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1497      final r-factor (free) = 0.1492          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5971 = 0.11 * 1.00 * 5.1373 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5941 = 0.11 * 1.00 * 5.1173 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.716)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.22    68.01   16.45    None  None   None       |
|    all(noH): 2823   0      2.22    68.01   16.45    None  None   None       |
|    Sol.    : 438    0      5.70    68.01   36.08    None  None   None       |
|    Mac.    : 2385   0      2.22    66.31   12.85    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:     2.215 -   8.794:  630   |   5:    35.111 -  41.690:  130        |
|      1:     8.794 -  15.373: 1276   |   6:    41.690 -  48.269:   84        |
|      2:    15.373 -  21.953:  365   |   7:    48.269 -  54.848:   66        |
|      3:    21.953 -  28.532:  135   |   8:    54.848 -  61.427:   23        |
|      4:    28.532 -  35.111:  109   |   9:    61.427 -  68.006:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1492             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1493             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1493   ksol= 0.31   Bsol= 38.49   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.57,-1.66,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116261                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1493   ksol= 0.32   Bsol= 40.23   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.52,-1.38,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115981                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.994511              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.411  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.225279              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.646  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1493      final r-factor (free) = 0.1497          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1555 = 1.99 * 0.50 * 5.1169 + 1.00 * 0.0527                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1447 = 1.99 * 0.50 * 5.0976 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1497      final r-factor (free) = 0.1496          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1545 = 0.23 * 1.00 * 5.0976 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1540 = 0.23 * 1.00 * 5.0917 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.716)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.77    69.87   16.49    None  None   None       |
|    all(noH): 2823   0      1.77    69.87   16.49    None  None   None       |
|    Sol.    : 438    0      6.34    68.91   36.78    None  None   None       |
|    Mac.    : 2385   0      1.77    69.87   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.765 -   8.576:  618   |   5:    35.819 -  42.630:  124        |
|      1:     8.576 -  15.387: 1297   |   6:    42.630 -  49.440:   88        |
|      2:    15.387 -  22.198:  364   |   7:    49.440 -  56.251:   68        |
|      3:    22.198 -  29.008:  127   |   8:    56.251 -  63.062:   22        |
|      4:    29.008 -  35.819:  110   |   9:    63.062 -  69.872:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1069 r_free = 0.1496             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1497             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1497   ksol= 0.32   Bsol= 40.23   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.52,-1.38,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1497   ksol= 0.32   Bsol= 40.92   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.40,-1.20,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093461                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.296958              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.483  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.592222              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.043  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1497      final r-factor (free) = 0.1508          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3633 = 1.30 * 0.50 * 5.0922 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3603 = 1.30 * 0.50 * 5.1041 + 1.00 * 0.0505                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1508      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0296 = 0.59 * 1.00 * 5.1041 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0309 = 0.59 * 1.00 * 5.1042 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.716)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.90    75.93   16.66    None  None   None       |
|    all(noH): 2823   0      0.90    75.93   16.66    None  None   None       |
|    Sol.    : 438    0      6.36    70.77   38.07    None  None   None       |
|    Mac.    : 2385   0      0.90    75.93   12.72    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:     0.897 -   8.400:  638   |   5:    38.413 -  45.916:  122        |
|      1:     8.400 -  15.903: 1311   |   6:    45.916 -  53.420:   85        |
|      2:    15.903 -  23.407:  347   |   7:    53.420 -  60.923:   56        |
|      3:    23.407 -  30.910:  129   |   8:    60.923 -  68.426:   18        |
|      4:    30.910 -  38.413:  112   |   9:    68.426 -  75.930:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1517             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1517             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1517   ksol= 0.32   Bsol= 40.92   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.40,-1.20,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1516   ksol= 0.32   Bsol= 42.50   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.20,-1.01,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108890                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.126636              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.365  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.028025              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.846  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4786 = 2.13 * 0.50 * 5.1049 + 1.00 * 0.0505                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4795 = 2.13 * 0.50 * 5.0979 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1055      final r-factor (work) = 0.1054          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2489 = 1.03 * 1.00 * 5.0979 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2463 = 1.03 * 1.00 * 5.0950 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.716)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.51    77.02   16.52    None  None   None       |
|    all(noH): 2823   0      0.51    77.02   16.52    None  None   None       |
|    Sol.    : 438    0      5.97    71.11   38.16    None  None   None       |
|    Mac.    : 2385   0      0.51    77.02   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.509 -   8.160:  622   |   5:    38.764 -  46.415:  118        |
|      1:     8.160 -  15.811: 1327   |   6:    46.415 -  54.066:   85        |
|      2:    15.811 -  23.462:  352   |   7:    54.066 -  61.717:   56        |
|      3:    23.462 -  31.113:  127   |   8:    61.717 -  69.368:   16        |
|      4:    31.113 -  38.764:  115   |   9:    69.368 -  77.019:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1054 r_free = 0.1521             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1054 r_free = 0.1521             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1521   ksol= 0.32   Bsol= 42.50   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.20,-1.01,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.097623                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7257 0.99   1380  153 0.0987 0.1249       5.378      5.5112|
|  2:  4.7257 -  3.7710 0.99   1312  149 0.0829 0.1120       5.419      5.6255|
|  3:  3.7710 -  3.3003 0.99   1305  145 0.1018 0.1473      5.4458      5.8274|
|  4:  3.3003 -  3.0012 0.99   1290  136 0.1130 0.1477      5.3988      5.5373|
|  5:  3.0012 -  2.7876 0.99   1269  144 0.1222 0.1663      5.2751      5.5144|
|  6:  2.7876 -  2.6242 0.99   1275  145 0.1124 0.1794      5.1674      5.4264|
|  7:  2.6242 -  2.4934 0.99   1280  143 0.1166 0.1586      5.1098      5.3283|
|  8:  2.4934 -  2.3853 0.98   1263  135 0.1099 0.1654      5.0293      5.3072|
|  9:  2.3853 -  2.2938 0.98   1251  143 0.1085 0.1702      4.9764      5.2533|
| 10:  2.2938 -  2.2149 0.99   1264  136 0.1037 0.1656      4.9145      5.1752|
| 11:  2.2149 -  2.1459 0.98   1262  142 0.1048 0.1643      4.8922      5.1873|
| 12:  2.1459 -  2.0847 0.97   1226  139 0.1048 0.1571      4.8305      5.1776|
| 13:  2.0847 -  2.0300 1.00   1264  137 0.1013 0.1670      4.7397      5.0287|
| 14:  2.0300 -  1.9806 0.78    989  112 0.0976 0.1733      4.6197      4.9243|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.7257  1380   153  0.94   9.15   0.98     0.95       7054.34|
|  2:  4.7257 -  3.7710  1312   149  0.95   7.71   1.02     1.01       8782.60|
|  3:  3.7710 -  3.3003  1305   145  0.94  10.74   1.03     1.02       9771.33|
|  4:  3.3003 -  3.0012  1290   136  0.93  12.62   1.01     0.99       9333.89|
|  5:  3.0012 -  2.7876  1269   144  0.91  15.04   1.00     0.97       7661.94|
|  6:  2.7876 -  2.6242  1275   145  0.91  15.23   0.98     0.96       6596.43|
|  7:  2.6242 -  2.4934  1280   143  0.91  14.93   0.98     0.95       5699.49|
|  8:  2.4934 -  2.3853  1263   135  0.92  13.95   0.99     0.97       4841.75|
|  9:  2.3853 -  2.2938  1251   143  0.92  14.41   1.00     0.98       4559.53|
| 10:  2.2938 -  2.2149  1264   136  0.91  14.95   0.99     0.95       4058.11|
| 11:  2.2149 -  2.1459  1262   142  0.91  15.08   0.99     0.96       4070.22|
| 12:  2.1459 -  2.0847  1226   139  0.91  14.65   1.01     0.99       3639.02|
| 13:  2.0847 -  2.0300  1264   137  0.91  14.63   0.99     0.98       3066.75|
| 14:  2.0300 -  1.9806   989   112  0.92  13.61   0.97     0.94       2335.06|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2335.06 max =         9771.33 mean =      5911.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.28|
|phase err.(test): min =        0.00 max =           89.89 mean =        12.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1521   ksol= 0.32   Bsol= 42.48   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.97,-0.78,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097722                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1521   ksol= 0.32   Bsol= 42.48   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.97,-0.78,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097722                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7257 0.99   1380  153 0.0987 0.1250      5.3786       5.512|
|  2:  4.7257 -  3.7710 0.99   1312  149 0.0829 0.1120      5.4195      5.6253|
|  3:  3.7710 -  3.3003 0.99   1305  145 0.1018 0.1473      5.4458      5.8276|
|  4:  3.3003 -  3.0012 0.99   1290  136 0.1129 0.1477      5.3987      5.5373|
|  5:  3.0012 -  2.7876 0.99   1269  144 0.1222 0.1662       5.275      5.5142|
|  6:  2.7876 -  2.6242 0.99   1275  145 0.1124 0.1794      5.1674      5.4263|
|  7:  2.6242 -  2.4934 0.99   1280  143 0.1166 0.1586      5.1099      5.3283|
|  8:  2.4934 -  2.3853 0.98   1263  135 0.1099 0.1653      5.0293       5.307|
|  9:  2.3853 -  2.2938 0.98   1251  143 0.1085 0.1702      4.9765      5.2532|
| 10:  2.2938 -  2.2149 0.99   1264  136 0.1037 0.1656      4.9147      5.1752|
| 11:  2.2149 -  2.1459 0.98   1262  142 0.1048 0.1643      4.8922      5.1872|
| 12:  2.1459 -  2.0847 0.97   1226  139 0.1048 0.1571      4.8305      5.1776|
| 13:  2.0847 -  2.0300 1.00   1264  137 0.1013 0.1670      4.7397      5.0285|
| 14:  2.0300 -  1.9806 0.78    989  112 0.0976 0.1733      4.6198      4.9244|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.7257  1380   153  0.94   9.16   0.98     0.95       7063.20|
|  2:  4.7257 -  3.7710  1312   149  0.95   7.71   1.02     1.01       8789.33|
|  3:  3.7710 -  3.3003  1305   145  0.94  10.74   1.03     1.02       9770.54|
|  4:  3.3003 -  3.0012  1290   136  0.93  12.62   1.01     1.00       9331.25|
|  5:  3.0012 -  2.7876  1269   144  0.91  15.04   1.01     0.98       7660.05|
|  6:  2.7876 -  2.6242  1275   145  0.91  15.23   0.99     0.96       6595.16|
|  7:  2.6242 -  2.4934  1280   143  0.91  14.94   0.99     0.96       5698.88|
|  8:  2.4934 -  2.3853  1263   135  0.92  13.95   1.00     0.98       4841.63|
|  9:  2.3853 -  2.2938  1251   143  0.92  14.41   1.01     0.98       4560.13|
| 10:  2.2938 -  2.2149  1264   136  0.91  14.95   1.00     0.96       4058.76|
| 11:  2.2149 -  2.1459  1262   142  0.91  15.08   1.00     0.98       4070.50|
| 12:  2.1459 -  2.0847  1226   139  0.91  14.66   1.02     1.00       3639.06|
| 13:  2.0847 -  2.0300  1264   137  0.91  14.63   1.01     0.99       3066.75|
| 14:  2.0300 -  1.9806   989   112  0.92  13.61   0.98     0.95       2335.49|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2335.49 max =         9770.54 mean =      5911.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.28|
|phase err.(test): min =        0.00 max =           89.90 mean =        12.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.716)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    77.00   16.50    None  None   None       |
|    all(noH): 2823   0      0.49    77.00   16.50    None  None   None       |
|    Sol.    : 438    0      5.95    71.09   38.15    None  None   None       |
|    Mac.    : 2385   0      0.49    77.00   12.53    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:     0.492 -   8.143:  622   |   5:    38.748 -  46.399:  118        |
|      1:     8.143 -  15.794: 1327   |   6:    46.399 -  54.050:   85        |
|      2:    15.794 -  23.446:  352   |   7:    54.050 -  61.701:   56        |
|      3:    23.446 -  31.097:  127   |   8:    61.701 -  69.352:   16        |
|      4:    31.097 -  38.748:  115   |   9:    69.352 -  77.003:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 280         
Filter by distance & map next to the model:
   mapped sites are within: 0.411 - 4.679
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 276 from: 280
   mapped sites are within: 0.701 - 4.679

peak=    5.499 closest distance to " O   HOH Z 142 " =    1.790
peak=    5.466 closest distance to " CG  PRO A  54 " =    1.260
peak=    5.438 closest distance to " CB  ARG A 275 " =    0.933
peak=    5.387 closest distance to " O   HOH Z 126 " =    1.958
peak=    5.336 closest distance to " NH2 ARG A  56 " =    2.120
peak=    5.125 closest distance to " NE2 GLN A  11 " =    1.084
peak=    4.939 closest distance to " CB  SER A  63 " =    1.178
peak=    4.865 closest distance to " CB  GLN A 223 " =    1.443
peak=    4.841 closest distance to " O   HOH Z 250 " =    2.421
peak=    4.833 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.795 closest distance to " O   HOH Z  78 " =    1.794
peak=    4.733 closest distance to " CB  GLU A 152 " =    1.234
peak=    4.547 closest distance to " O   HOH Z 427 " =    2.840
peak=    4.542 closest distance to " O   HOH Z 369 " =    2.107
peak=    4.485 closest distance to " O   HOH Z  15 " =    2.265
peak=    4.462 closest distance to " CB  PRO A  54 " =    0.953
peak=    4.439 closest distance to " C   PRO A 198 " =    1.414
peak=    4.422 closest distance to " O   HOH Z 234 " =    3.637
peak=    4.417 closest distance to " O   HOH Z 236 " =    2.088
peak=    4.399 closest distance to " ND2 ASN A 187 " =    1.462
peak=    4.386 closest distance to " CB  ARG A  79 " =    1.341
peak=    4.351 closest distance to " O   HOH Z  78 " =    2.117
peak=    4.350 closest distance to " O   HOH Z 250 " =    1.512
peak=    4.344 closest distance to " CB  ASN A 148 " =    1.405
peak=    4.339 closest distance to " O   HOH Z 209 " =    2.290
peak=    4.338 closest distance to " CA  TYR A  30 " =    0.912
peak=    4.334 closest distance to " O   HOH Z 303 " =    2.068
peak=    4.327 closest distance to " CB  VAL A 265 " =    1.273
peak=    4.232 closest distance to " O   HOH Z 402 " =    1.358
peak=    4.219 closest distance to " O   HOH Z 298 " =    1.822
peak=    4.203 closest distance to " CG2 VAL A 257 " =    0.891
peak=    4.198 closest distance to " CB  ARG A 190 " =    1.652
peak=    4.180 closest distance to " O   HOH Z 272 " =    1.838
peak=    4.161 closest distance to " O   HOH Z 346 " =    1.659
peak=    4.160 closest distance to " O   HOH Z 193 " =    1.843
peak=    4.154 closest distance to " O   HOH Z  61 " =    1.650
peak=    4.154 closest distance to " O   HOH Z 189 " =    2.254
peak=    4.142 closest distance to " CB  TYR A 169 " =    0.765
peak=    4.141 closest distance to " CD2 TRP A 179 " =    1.344
peak=    4.131 closest distance to " O   HOH Z 158 " =    2.997
peak=    4.122 closest distance to " O   HOH Z 203 " =    1.711
peak=    4.110 closest distance to " NZ  LYS A 117 " =    3.180
peak=    4.078 closest distance to " O   HOH Z 248 " =    1.629
peak=    4.070 closest distance to " CG  PRO A 198 " =    1.271
peak=    4.050 closest distance to " O   HOH Z  40 " =    1.648
peak=    4.037 closest distance to " O   HOH Z 392 " =    3.091
peak=    4.016 closest distance to " O   SER A  87 " =    2.149
peak=    4.000 closest distance to " O   HOH Z  43 " =    1.914
peak=    3.989 closest distance to " O   HOH Z  44 " =    1.799
peak=    3.962 closest distance to " O   HOH Z 403 " =    1.659
peak=    3.955 closest distance to " O   HOH Z  97 " =    2.553
peak=    3.953 closest distance to " OD1 ASN A  69 " =    2.557
peak=    3.942 closest distance to " CA  ASN A 215 " =    1.151
peak=    3.937 closest distance to " CG  PRO A 243 " =    1.063
peak=    3.933 closest distance to " OG ASER A 258 " =    3.069
peak=    3.896 closest distance to " O   HOH Z 245 " =    1.316
peak=    3.883 closest distance to " CB  TRP A 266 " =    1.035
peak=    3.865 closest distance to " CB  LEU A 228 " =    1.108
peak=    3.861 closest distance to " O   HOH Z 389 " =    1.814
peak=    3.857 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.850 closest distance to " O   HOH Z   1 " =    1.974
peak=    3.820 closest distance to " CG  ARG A  66 " =    2.596
peak=    3.808 closest distance to " CG1 ILE A  33 " =    1.218
peak=    3.792 closest distance to " O   HOH Z 425 " =    2.061
peak=    3.784 closest distance to " O   HOH Z 417 " =    3.204
peak=    3.778 closest distance to " CB  GLU A 128 " =    1.035
peak=    3.776 closest distance to " O   HOH Z 172 " =    3.305
peak=    3.773 closest distance to " CZ  PHE A 218 " =    1.065
peak=    3.769 closest distance to " CG1BVAL A  72 " =    1.556
peak=    3.768 closest distance to " O   HOH Z 298 " =    2.531
peak=    3.766 closest distance to " CB  VAL A 202 " =    1.560
peak=    3.761 closest distance to " CB  SER A   3 " =    1.298
peak=    3.757 closest distance to " O   HOH Z   9 " =    2.094
peak=    3.748 closest distance to " CE  LYS A  76 " =    0.816
peak=    3.747 closest distance to " O   HOH Z 173 " =    1.885
peak=    3.746 closest distance to " O   HOH Z  10 " =    1.842
peak=    3.746 closest distance to " O   HOH Z 371 " =    3.117
peak=    3.746 closest distance to " O   HOH Z 368 " =    2.019
peak=    3.732 closest distance to " OE1 GLU A   2 " =    2.175
peak=    3.727 closest distance to " O   HOH Z 128 " =    2.065
peak=    3.726 closest distance to " O   HOH Z 291 " =    1.479
peak=    3.724 closest distance to " O   HOH Z 419 " =    2.053
peak=    3.712 closest distance to " O   HOH Z 128 " =    2.193
peak=    3.710 closest distance to " O   HOH Z 407 " =    2.398
peak=    3.701 closest distance to " O   HOH Z 261 " =    2.132
peak=    3.690 closest distance to " O   HOH Z  66 " =    2.124
peak=    3.679 closest distance to " CG2 ILE A 120 " =    1.119
peak=    3.670 closest distance to " O   HOH Z  59 " =    1.808
peak=    3.655 closest distance to " OD2 ASP A 286 " =    2.772
peak=    3.640 closest distance to " O   HOH Z 368 " =    3.621
peak=    3.631 closest distance to " CB  SER A  26 " =    1.593
peak=    3.629 closest distance to " O   HOH Z 280 " =    2.986
peak=    3.626 closest distance to " O   HOH Z 371 " =    1.719
peak=    3.617 closest distance to " CB  GLU A 277 " =    3.521
peak=    3.612 closest distance to " CB  TRP A 179 " =    1.305
peak=    3.605 closest distance to " O   HOH Z 337 " =    3.635
peak=    3.605 closest distance to " O   HOH Z  54 " =    1.679
peak=    3.593 closest distance to " O   HOH Z 344 " =    3.175
peak=    3.589 closest distance to " NH1AARG A 145 " =    1.181
peak=    3.579 closest distance to " O   HOH Z 423 " =    1.923
peak=    3.574 closest distance to " O   HOH Z 132 " =    2.400
peak=    3.572 closest distance to " O   HOH Z  97 " =    1.973
peak=    3.570 closest distance to " CB  GLN A  89 " =    1.399
peak=    3.569 closest distance to " CB  ARG A 139 " =    0.988
peak=    3.566 closest distance to " O   HOH Z  19 " =    2.454
peak=    3.560 closest distance to " O   HOH Z  61 " =    1.470
peak=    3.552 closest distance to " O   HOH Z 305 " =    3.630
peak=    3.544 closest distance to " CD1 ILE A 106 " =    0.823
peak=    3.544 closest distance to " N   ASN A  39 " =    1.208
peak=    3.542 closest distance to " CD2 LEU A 255 " =    1.398
peak=    3.533 closest distance to " CA  ARG A  36 " =    0.979
peak=    3.533 closest distance to " CD2 LEU A 297 " =    0.897
peak=    3.529 closest distance to " CA  ALA A  21 " =    1.128
peak=    3.529 closest distance to " O   HOH Z 133 " =    2.831
peak=    3.524 closest distance to " OG1 THR A 294 " =    2.382
peak=    3.522 closest distance to " CD BLYS A 290 " =    1.218
peak=    3.519 closest distance to " CD  ARG A 159 " =    0.702
peak=    3.515 closest distance to " O   HOH Z 193 " =    1.962
peak=    3.504 closest distance to " NH2BARG A 145 " =    1.996
peak=    3.504 closest distance to " CA  ARG A 195 " =    1.266
peak=    3.503 closest distance to " OG BSER A 164 " =    2.272
peak=    3.500 closest distance to " CA  ALA A 233 " =    1.098
peak=    3.482 closest distance to " NE2 GLN A  73 " =    3.714
peak=    3.476 closest distance to " CB  SER A 212 " =    1.066
peak=    3.474 closest distance to " O   HOH Z 180 " =    2.233
peak=    3.472 closest distance to " O   HOH Z  88 " =    2.530
peak=    3.471 closest distance to " CA  THR A 221 " =    1.000
peak=    3.470 closest distance to " O   HOH Z 426 " =    1.615
peak=    3.468 closest distance to " O   HOH Z 329 " =    3.888
peak=    3.467 closest distance to " O   HOH Z 327 " =    1.575
peak=    3.465 closest distance to " O   HOH Z 313 " =    1.912
peak=    3.465 closest distance to " O   HOH Z 193 " =    1.626
peak=    3.464 closest distance to " CB  ASN A 110 " =    1.082
peak=    3.458 closest distance to " O   HOH Z 261 " =    1.637
peak=    3.455 closest distance to " O   HOH Z 148 " =    3.384
peak=    3.447 closest distance to " O   HOH Z 214 " =    2.177
peak=    3.439 closest distance to " O   HOH Z 147 " =    1.747
peak=    3.434 closest distance to " O   HOH Z 273 " =    2.744
peak=    3.433 closest distance to " CA  LYS A 117 " =    1.212
peak=    3.432 closest distance to " N   ARG A 156 " =    1.316
peak=    3.424 closest distance to " O   HOH Z 421 " =    1.712
peak=    3.422 closest distance to " O   HOH Z 187 " =    2.233
peak=    3.416 closest distance to " O   HOH Z 185 " =    1.774
peak=    3.414 closest distance to " O   HOH Z 234 " =    1.897
peak=    3.412 closest distance to " CB  MET A  47 " =    1.088
peak=    3.411 closest distance to " CD  ARG A 269 " =    0.956
peak=    3.410 closest distance to " N   TYR A 116 " =    1.574
peak=    3.408 closest distance to " O   HOH Z  44 " =    3.024
peak=    3.403 closest distance to " CA  ALA A  84 " =    1.229
peak=    3.401 closest distance to " CG2 ILE A  20 " =    1.566
peak=    3.400 closest distance to " CB  GLU A  46 " =    1.006
peak=    3.400 closest distance to " O  BHOH Z 338 " =    2.338
peak=    3.398 closest distance to " CB  ALA A 291 " =    1.332
peak=    3.391 closest distance to " O   ALA A   1 " =    1.695
peak=    3.390 closest distance to " CB  ALA A  34 " =    1.130
peak=    3.387 closest distance to " CG1 VAL A 153 " =    0.949
peak=    3.386 closest distance to " CB  ALA A 248 " =    1.352
peak=    3.386 closest distance to " O   HOH Z  21 " =    1.768
peak=    3.382 closest distance to " CB  SER A  62 " =    1.273
peak=    3.380 closest distance to " O   HOH Z 345 " =    3.332
peak=    3.379 closest distance to " O   HOH Z 435 " =    1.920
peak=    3.377 closest distance to " O   HOH Z  64 " =    2.211
peak=    3.375 closest distance to " CB  HIS A 108 " =    0.813
peak=    3.374 closest distance to " CB  THR A  31 " =    1.686
peak=    3.373 closest distance to " CB  ASN A  39 " =    0.876
peak=    3.368 closest distance to " CG  LYS A  76 " =    0.963
peak=    3.367 closest distance to " NE2 GLN A  77 " =    3.144
peak=    3.365 closest distance to " CB  THR A 157 " =    1.090
peak=    3.356 closest distance to " CB  TYR A 116 " =    0.777
peak=    3.340 closest distance to " CA  PHE A 283 " =    1.320
peak=    3.340 closest distance to " O   HOH Z 365 " =    2.915
peak=    3.338 closest distance to " CB  SER A  62 " =    0.889
peak=    3.332 closest distance to " O   HOH Z 213 " =    1.722
peak=    3.323 closest distance to " CG AARG A 275 " =    1.075
peak=    3.321 closest distance to " O   HOH Z 433 " =    1.806
peak=    3.319 closest distance to " CB  ILE A 120 " =    1.281
peak=    3.315 closest distance to " C   ILE A 106 " =    1.877
peak=    3.315 closest distance to " CA  ASP A 162 " =    1.070
peak=    3.314 closest distance to " CB  ASN A 142 " =    1.067
peak=    3.309 closest distance to " O   ASN A  74 " =    1.572
peak=    3.306 closest distance to " O   HOH Z  85 " =    2.322
peak=    3.301 closest distance to " O   HOH Z 175 " =    2.136
peak=    3.300 closest distance to " O   HOH Z 245 " =    2.182
peak=    3.298 closest distance to " ND2 ASN A 110 " =    1.677
peak=    3.296 closest distance to " CA  ALA A 158 " =    1.315
peak=    3.295 closest distance to " O   HOH Z  88 " =    2.454
peak=    3.292 closest distance to " O   HOH Z 403 " =    1.329
peak=    3.287 closest distance to " O   HOH Z 336 " =    1.786
peak=    3.285 closest distance to " CB  LYS A 290 " =    0.967
peak=    3.283 closest distance to " CB  GLN A  88 " =    1.189
peak=    3.283 closest distance to " CG  LEU A 167 " =    1.277
peak=    3.282 closest distance to " CA  ALA A  51 " =    0.885
peak=    3.279 closest distance to " CA  ALA A 291 " =    0.804
peak=    3.279 closest distance to " O   HOH Z 406 " =    1.525
peak=    3.273 closest distance to " O   HOH Z 353 " =    2.642
peak=    3.271 closest distance to " CB  LYS A 117 " =    1.230
peak=    3.270 closest distance to " CB  SER A 141 " =    1.083
peak=    3.264 closest distance to " CA  THR A 264 " =    0.885
peak=    3.260 closest distance to " O   HOH Z 219 " =    2.070
peak=    3.259 closest distance to " CA  ALA A  43 " =    1.249
peak=    3.254 closest distance to " O   HOH Z 411 " =    3.787
peak=    3.250 closest distance to " N   PHE A 130 " =    1.269
peak=    3.248 closest distance to " CE1 TYR A 186 " =    1.286
peak=    3.246 closest distance to " O   HOH Z 299 " =    4.402
peak=    3.244 closest distance to " CA  MET A 105 " =    1.000
peak=    3.242 closest distance to " CZ2 TRP A 179 " =    1.738
peak=    3.241 closest distance to " CD  LYS A 166 " =    1.218
peak=    3.240 closest distance to " CG  MET A 113 " =    1.105
peak=    3.239 closest distance to " O   HOH Z 285 " =    2.743
peak=    3.237 closest distance to " O   HOH Z 359 " =    1.373
peak=    3.237 closest distance to " CD1 LEU A 300 " =    1.313
peak=    3.236 closest distance to " CG2 THR A 221 " =    1.102
peak=    3.235 closest distance to " CG  GLN A  77 " =    2.125
peak=    3.234 closest distance to " O   HOH Z 286 " =    2.230
peak=    3.232 closest distance to " CD  LYS A 119 " =    1.303
peak=    3.231 closest distance to " NH1BARG A 145 " =    1.290
peak=    3.226 closest distance to " CD1 ILE A 263 " =    1.332
peak=    3.221 closest distance to " ND1 HIS A  86 " =    1.791
peak=    3.220 closest distance to " O   HOH Z   1 " =    1.616
peak=    3.217 closest distance to " O   HOH Z  80 " =    1.689
peak=    3.212 closest distance to " N   ASN A 127 " =    1.206
peak=    3.212 closest distance to " O   HOH Z 213 " =    1.754
peak=    3.208 closest distance to " CG1 ILE A 120 " =    1.093
peak=    3.198 closest distance to " O   HOH Z 236 " =    1.396
peak=    3.195 closest distance to " CB  ALA A   9 " =    1.524
peak=    3.194 closest distance to " NE  ARG A  24 " =    1.949
peak=    3.189 closest distance to " ND2 ASN A 249 " =    0.872
peak=    3.188 closest distance to " O   HOH Z 227 " =    2.118
peak=    3.188 closest distance to " O   HOH Z 325 " =    3.743
peak=    3.185 closest distance to " O   HOH Z 357 " =    1.818
peak=    3.179 closest distance to " O   HOH Z 302 " =    1.949
peak=    3.179 closest distance to " CD2 HIS A  81 " =    1.131
peak=    3.176 closest distance to " O   HOH Z 188 " =    1.963
peak=    3.175 closest distance to " O   HOH Z 135 " =    1.656
peak=    3.175 closest distance to " CD1 LEU A  96 " =    0.764
peak=    3.172 closest distance to " CG  MET A 185 " =    1.127
peak=    3.171 closest distance to " CA  ASN A 217 " =    1.226
peak=    3.169 closest distance to " O   HOH Z 227 " =    1.527
peak=    3.169 closest distance to " CD  ARG A 156 " =    1.564
peak=    3.168 closest distance to " CB  THR A 279 " =    1.685
peak=    3.164 closest distance to " O   HOH Z  47 " =    1.800
peak=    3.164 closest distance to " O   HOH Z 261 " =    2.309
peak=    3.163 closest distance to " O   HOH Z 409 " =    2.957
peak=    3.162 closest distance to " CB  ASN A 224 " =    0.996
peak=    3.158 closest distance to " O   HOH Z 265 " =    2.431
peak=    3.157 closest distance to " CA  SER A  87 " =    1.062
peak=    3.148 closest distance to " CG2 VAL A 197 " =    1.098
peak=    3.143 closest distance to " CB  ALA A   1 " =    4.679
peak=    3.142 closest distance to " O   HOH Z 279 " =    2.131
peak=    3.141 closest distance to " CG  GLN A  11 " =    1.665
peak=    3.139 closest distance to " CA  TYR A 116 " =    1.314
peak=    3.135 closest distance to " O   HOH Z 271 " =    2.381
peak=    3.134 closest distance to " CA  GLY A  80 " =    0.724
peak=    3.128 closest distance to " CE AMET A  47 " =    1.390
peak=    3.127 closest distance to " O   HOH Z 423 " =    2.947
peak=    3.123 closest distance to " CG  GLN A  89 " =    1.543
peak=    3.120 closest distance to " CB  VAL A 126 " =    1.108
peak=    3.115 closest distance to " CB  VAL A 268 " =    0.843
peak=    3.113 closest distance to " CG  LYS A  76 " =    1.628
peak=    3.113 closest distance to " O   THR A 220 " =    1.310
peak=    3.111 closest distance to " CB  GLN A 278 " =    0.844
peak=    3.108 closest distance to " CG1 ILE A  49 " =    1.399
peak=    3.107 closest distance to " CB  ASN A 215 " =    1.109
peak=    3.102 closest distance to " CB  SER A 216 " =    0.779
peak=    3.097 closest distance to " CB  LEU A 255 " =    0.788
peak=    3.097 closest distance to " NH1 ARG A 138 " =    1.168
peak=    3.090 closest distance to " CA  ALA A 299 " =    0.941
peak=    3.086 closest distance to " CB  PHE A 204 " =    0.701
peak=    3.084 closest distance to " CA  SER A 146 " =    1.716
peak=    3.081 closest distance to " NE2 HIS A 207 " =    1.353
peak=    3.076 closest distance to " OD1BASN A 224 " =    2.302
peak=    3.051 closest distance to " CA  ARG A 102 " =    1.001
peak=    3.049 closest distance to " CB  LEU A 300 " =    0.906
peak=    3.038 closest distance to " O   HOH Z 266 " =    3.376
peak=    3.033 closest distance to " N   ASP A 162 " =    1.257
peak=    3.025 closest distance to " O   HOH Z 391 " =    2.903

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 189         
Filter by distance & map next to the model:
   mapped sites are within: 0.806 - 5.879
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 189
   mapped sites are within: 0.806 - 5.879

peak=   -4.814 closest distance to " O   HOH Z 266 " =    4.994
peak=   -4.497 closest distance to " CB  PRO A 243 " =    2.671
peak=   -4.491 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.463 closest distance to " OG BSER A 134 " =    1.232
peak=   -4.447 closest distance to " CG  GLN A 223 " =    1.901
peak=   -4.433 closest distance to " C   HIS A 108 " =    1.094
peak=   -4.425 closest distance to " CD  GLN A  58 " =    1.047
peak=   -4.342 closest distance to " O   VAL A  67 " =    2.663
peak=   -4.325 closest distance to " CA  VAL A  67 " =    2.892
peak=   -4.318 closest distance to " O   HOH Z 290 " =    1.140
peak=   -4.294 closest distance to " CG1 VAL A 112 " =    2.794
peak=   -4.240 closest distance to " SG  CYS A 254 " =    3.442
peak=   -4.148 closest distance to " O   HOH Z 377 " =    2.083
peak=   -4.086 closest distance to " CE  MET A 105 " =    2.412
peak=   -4.072 closest distance to " O   HOH Z 372 " =    2.357
peak=   -4.069 closest distance to " O   HOH Z 231 " =    2.271
peak=   -4.040 closest distance to " CD  ARG A 139 " =    1.529
peak=   -4.035 closest distance to " O   HOH Z 435 " =    2.777
peak=   -4.020 closest distance to " O   HOH Z 389 " =    1.935
peak=   -4.002 closest distance to " O   HOH Z 198 " =    1.906
peak=   -4.000 closest distance to " ND2 ASN A  45 " =    1.771
peak=   -3.928 closest distance to " OXT GLY A 302 " =    2.765
peak=   -3.911 closest distance to " N   ALA A  43 " =    2.578
peak=   -3.883 closest distance to " CZ3 TRP A 179 " =    1.201
peak=   -3.842 closest distance to " CD2 PHE A 192 " =    2.032
peak=   -3.839 closest distance to " CB  ALA A 291 " =    2.240
peak=   -3.829 closest distance to " CE2 PHE A 218 " =    2.430
peak=   -3.814 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.812 closest distance to " O   HOH Z 313 " =    1.876
peak=   -3.810 closest distance to " OG  SER A  97 " =    2.192
peak=   -3.806 closest distance to " O   HOH Z 114 " =    3.029
peak=   -3.806 closest distance to " O   HOH Z 211 " =    1.657
peak=   -3.803 closest distance to " CB  ASN A  39 " =    2.322
peak=   -3.787 closest distance to " O   HOH Z 353 " =    2.224
peak=   -3.786 closest distance to " O   HOH Z 185 " =    2.242
peak=   -3.782 closest distance to " O   HOH Z 351 " =    1.521
peak=   -3.776 closest distance to " O   HOH Z 407 " =    2.879
peak=   -3.764 closest distance to " CZ  TYR A 169 " =    1.795
peak=   -3.762 closest distance to " CG  PHE A 283 " =    2.693
peak=   -3.747 closest distance to " O   ALA A 161 " =    1.676
peak=   -3.726 closest distance to " CB  ALA A 291 " =    2.379
peak=   -3.725 closest distance to " OD2 ASP A 191 " =    1.403
peak=   -3.706 closest distance to " CG2 ILE A 263 " =    2.224
peak=   -3.705 closest distance to " CZ  PHE A  59 " =    1.490
peak=   -3.693 closest distance to " OD1 ASN A 187 " =    1.606
peak=   -3.685 closest distance to " CD1 PHE A  59 " =    1.936
peak=   -3.682 closest distance to " CB  ALA A 161 " =    2.560
peak=   -3.676 closest distance to " CA  GLY A 133 " =    1.966
peak=   -3.669 closest distance to " N   ALA A 248 " =    1.705
peak=   -3.667 closest distance to " O   PRO A 163 " =    2.012
peak=   -3.667 closest distance to " CE2 TYR A  30 " =    2.734
peak=   -3.628 closest distance to " CG  ARG A 269 " =    2.286
peak=   -3.624 closest distance to " O   HOH Z  10 " =    1.458
peak=   -3.611 closest distance to " O   HOH Z 126 " =    1.897
peak=   -3.600 closest distance to " O   HOH Z 196 " =    2.097
peak=   -3.596 closest distance to " CB  ALA A 248 " =    2.312
peak=   -3.581 closest distance to " CA  GLY A 203 " =    2.344
peak=   -3.578 closest distance to " O   PRO A 198 " =    1.255
peak=   -3.570 closest distance to " N   GLN A  58 " =    1.713
peak=   -3.563 closest distance to " O   HOH Z  60 " =    2.304
peak=   -3.561 closest distance to " O   PHE A 218 " =    1.583
peak=   -3.536 closest distance to " O   HOH Z  13 " =    1.575
peak=   -3.532 closest distance to " NE2 GLN A 278 " =    1.709
peak=   -3.528 closest distance to " N   ASP A 286 " =    2.349
peak=   -3.527 closest distance to " ND2 ASN A 187 " =    1.541
peak=   -3.527 closest distance to " OD2 ASP A 171 " =    2.303
peak=   -3.520 closest distance to " CD1 LEU A 101 " =    2.259
peak=   -3.516 closest distance to " O   HOH Z 298 " =    1.265
peak=   -3.508 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.507 closest distance to " O   HOH Z  43 " =    1.772
peak=   -3.501 closest distance to " O   SER A 135 " =    1.445
peak=   -3.491 closest distance to " O   HOH Z 193 " =    2.046
peak=   -3.477 closest distance to " O   ARG A 145 " =    1.541
peak=   -3.471 closest distance to " CG1 VAL A 230 " =    2.053
peak=   -3.471 closest distance to " O   SER A 210 " =    2.001
peak=   -3.470 closest distance to " CB  ASP A 132 " =    2.290
peak=   -3.465 closest distance to " NH2AARG A 275 " =    5.141
peak=   -3.463 closest distance to " CB  PHE A 208 " =    2.208
peak=   -3.461 closest distance to " O   HOH Z 165 " =    2.091
peak=   -3.458 closest distance to " O   SER A  95 " =    1.490
peak=   -3.453 closest distance to " O   HOH Z 102 " =    1.587
peak=   -3.453 closest distance to " CD1 LEU A 228 " =    2.093
peak=   -3.446 closest distance to " CB  ALA A 248 " =    2.151
peak=   -3.442 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.439 closest distance to " O   HOH Z 362 " =    5.879
peak=   -3.422 closest distance to " CG  ASP A 231 " =    0.806
peak=   -3.414 closest distance to " OD1 ASP A 191 " =    1.557
peak=   -3.407 closest distance to " NH1 ARG A 195 " =    2.599
peak=   -3.405 closest distance to " O   HOH Z  44 " =    2.222
peak=   -3.404 closest distance to " CB  GLN A  11 " =    1.805
peak=   -3.395 closest distance to " O   HOH Z 395 " =    5.195
peak=   -3.392 closest distance to " O   HOH Z 253 " =    3.799
peak=   -3.391 closest distance to " CB  PRO A 163 " =    2.452
peak=   -3.387 closest distance to " O   HOH Z  63 " =    1.676
peak=   -3.380 closest distance to " O   HOH Z 123 " =    2.302
peak=   -3.379 closest distance to " O   HOH Z 385 " =    2.092
peak=   -3.377 closest distance to " O   MET A  40 " =    2.725
peak=   -3.376 closest distance to " O   HOH Z 309 " =    2.549
peak=   -3.374 closest distance to " O   HOH Z 311 " =    3.656
peak=   -3.373 closest distance to " CA  GLY A  98 " =    1.872
peak=   -3.368 closest distance to " O   ALA A  51 " =    1.298
peak=   -3.365 closest distance to " O   HOH Z 198 " =    1.497
peak=   -3.364 closest distance to " CB  ALA A  43 " =    2.363
peak=   -3.362 closest distance to " OD1 ASN A 148 " =    1.560
peak=   -3.362 closest distance to " CD  GLU A 236 " =    1.031
peak=   -3.352 closest distance to " CD1 ILE A 239 " =    2.381
peak=   -3.351 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.342 closest distance to " O   HOH Z 166 " =    2.014
peak=   -3.336 closest distance to " CA  GLY A  57 " =    2.220
peak=   -3.332 closest distance to " CG1 VAL A  78 " =    3.152
peak=   -3.331 closest distance to " O   HOH Z 394 " =    1.461
peak=   -3.330 closest distance to " OG BSER A 134 " =    1.682
peak=   -3.329 closest distance to " SG ACYS A 201 " =    1.800
peak=   -3.320 closest distance to " CD1 LEU A   5 " =    2.486
peak=   -3.312 closest distance to " O   ALA A 292 " =    1.970
peak=   -3.310 closest distance to " O   HOH Z 134 " =    3.086
peak=   -3.307 closest distance to " C   PRO A  90 " =    1.542
peak=   -3.305 closest distance to " O   VAL A 189 " =    1.677
peak=   -3.302 closest distance to " O   VAL A 174 " =    2.110
peak=   -3.292 closest distance to " NE2 GLN A 194 " =    1.727
peak=   -3.289 closest distance to " CA  GLY A 241 " =    3.127
peak=   -3.285 closest distance to " O   HOH Z 243 " =    1.936
peak=   -3.285 closest distance to " CB  TRP A  85 " =    2.503
peak=   -3.282 closest distance to " O   VAL A 189 " =    2.610
peak=   -3.280 closest distance to " O   ALA A  10 " =    1.684
peak=   -3.267 closest distance to " OD2 ASP A  50 " =    1.609
peak=   -3.265 closest distance to " ND2 ASN A  45 " =    0.998
peak=   -3.265 closest distance to " CG  PHE A 283 " =    2.663
peak=   -3.263 closest distance to " CG  GLU A   2 " =    1.967
peak=   -3.255 closest distance to " OE2 GLU A 152 " =    1.238
peak=   -3.250 closest distance to " CD2 TYR A 293 " =    1.983
peak=   -3.249 closest distance to " O   HOH Z 166 " =    1.527
peak=   -3.243 closest distance to " O   HOH Z  38 " =    1.650
peak=   -3.241 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -3.236 closest distance to " C   MET A 188 " =    1.362
peak=   -3.234 closest distance to " OXT GLY A 302 " =    3.439
peak=   -3.233 closest distance to " O   HOH Z 244 " =    2.057
peak=   -3.232 closest distance to " CG  GLU A 277 " =    1.253
peak=   -3.230 closest distance to " CG1AVAL A  41 " =    2.777
peak=   -3.228 closest distance to " CD2 PHE A 225 " =    1.193
peak=   -3.218 closest distance to " CB  LEU A  83 " =    2.364
peak=   -3.214 closest distance to " OG  SER A  62 " =    1.636
peak=   -3.214 closest distance to " O   PRO A 198 " =    1.704
peak=   -3.213 closest distance to " NH2 ARG A  79 " =    1.594
peak=   -3.213 closest distance to " OD1 ASP A 191 " =    1.736
peak=   -3.203 closest distance to " CE3 TRP A 274 " =    2.338
peak=   -3.203 closest distance to " O   ALA A 180 " =    1.035
peak=   -3.203 closest distance to " C   LEU A 143 " =    1.032
peak=   -3.203 closest distance to " NH2BARG A 275 " =    1.983
peak=   -3.201 closest distance to " O   SER A 146 " =    1.138
peak=   -3.198 closest distance to " O   GLN A 240 " =    2.395
peak=   -3.196 closest distance to " CB  ASP A 286 " =    1.757
peak=   -3.196 closest distance to " CB  ASP A 286 " =    2.138
peak=   -3.196 closest distance to " O   HOH Z 263 " =    2.964
peak=   -3.193 closest distance to " O   HOH Z 295 " =    1.579
peak=   -3.191 closest distance to " O   HOH Z 359 " =    3.183
peak=   -3.186 closest distance to " O   HOH Z  11 " =    1.740
peak=   -3.179 closest distance to " CG  GLU A 152 " =    1.087
peak=   -3.178 closest distance to " C   ALA A 158 " =    1.344
peak=   -3.177 closest distance to " O   HOH Z 421 " =    3.076
peak=   -3.170 closest distance to " CD2 PHE A  61 " =    2.569
peak=   -3.170 closest distance to " CG  ARG A  66 " =    2.458
peak=   -3.160 closest distance to " O   LEU A 167 " =    1.419
peak=   -3.157 closest distance to " O   HOH Z  91 " =    1.649
peak=   -3.156 closest distance to " O   HOH Z 111 " =    2.337
peak=   -3.155 closest distance to " O   HOH Z 139 " =    3.085
peak=   -3.154 closest distance to " N   PHE A  59 " =    1.853
peak=   -3.151 closest distance to " CG1 VAL A 250 " =    2.616
peak=   -3.146 closest distance to " O   GLN A 240 " =    2.013
peak=   -3.145 closest distance to " CG1 VAL A 125 " =    1.963
peak=   -3.145 closest distance to " N   ALA A 226 " =    2.010
peak=   -3.131 closest distance to " O   HOH Z   6 " =    1.466
peak=   -3.113 closest distance to " OE1 GLN A 194 " =    1.658
peak=   -3.108 closest distance to " O   ALA A  34 " =    2.320
peak=   -3.107 closest distance to " O   TRP A  70 " =    1.466
peak=   -3.103 closest distance to " O   HOH Z 140 " =    1.720
peak=   -3.097 closest distance to " O   HOH Z 174 " =    4.330
peak=   -3.096 closest distance to " C   VAL A 174 " =    1.755
peak=   -3.093 closest distance to " O   PRO A  90 " =    1.727
peak=   -3.091 closest distance to " O   HOH Z 427 " =    1.455
peak=   -3.079 closest distance to " CB  ASP A 132 " =    2.403
peak=   -3.078 closest distance to " O   HOH Z  73 " =    2.384
peak=   -3.075 closest distance to " O   SER A  22 " =    2.387
peak=   -3.068 closest distance to " O   HOH Z 137 " =    1.506
peak=   -3.057 closest distance to " O   HOH Z 281 " =    2.675
peak=   -3.046 closest distance to " OD1AASN A 224 " =    1.807
peak=   -3.033 closest distance to " CD2 LEU A 300 " =    2.883
peak=   -3.024 closest distance to " O   LYS A 289 " =    2.897
peak=   -3.018 closest distance to " O   HOH Z 210 " =    1.200

================= 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    :  0.2464 0.2449   5.795057e+00   5.774702e+00
   1_bss:  0.2291 0.2252   5.755732e+00   5.728213e+00
   1_xyz:  0.1338 0.1546   5.235503e+00   5.351243e+00
   1_adp:  0.1218 0.1570   5.175753e+00   5.373747e+00
   1_occ:  0.1214 0.1567   5.174170e+00   5.372991e+00
   2_bss:  0.1212 0.1557   5.172829e+00   5.367673e+00
   2_xyz:  0.1129 0.1497   5.119421e+00   5.331824e+00
   2_adp:  0.1125 0.1492   5.116559e+00   5.331032e+00
   2_occ:  0.1123 0.1493   5.116261e+00   5.331297e+00
   3_bss:  0.1122 0.1493   5.115981e+00   5.330949e+00
   3_xyz:  0.1080 0.1497   5.098111e+00   5.335456e+00
   3_adp:  0.1069 0.1496   5.093322e+00   5.337018e+00
   3_occ:  0.1068 0.1497   5.093486e+00   5.337507e+00
   4_bss:  0.1068 0.1497   5.093461e+00   5.337390e+00
   4_xyz:  0.1090 0.1508   5.109202e+00   5.346820e+00
   4_adp:  0.1083 0.1517   5.109114e+00   5.353156e+00
   4_occ:  0.1082 0.1517   5.109041e+00   5.353101e+00
   5_bss:  0.1081 0.1516   5.108890e+00   5.352786e+00
   5_xyz:  0.1055 0.1516   5.096897e+00   5.352147e+00
   5_adp:  0.1054 0.1521   5.097656e+00   5.355104e+00
   5_occ:  0.1054 0.1521   5.097623e+00   5.355070e+00
   5_bss:  0.1053 0.1521   5.097722e+00   5.355064e+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:  0.324  35.370  -1.926  -1.890  -1.639  -0.000  -0.000  -0.000
   1_xyz:  0.324  35.370  -1.926  -1.890  -1.639  -0.000  -0.000  -0.000
   1_adp:  0.324  35.370  -1.926  -1.890  -1.639  -0.000  -0.000  -0.000
   1_occ:  0.324  35.370  -1.926  -1.890  -1.639  -0.000  -0.000  -0.000
   2_bss:  0.311  38.490  -2.882  -2.566  -1.656  -0.000  -0.000  -0.000
   2_xyz:  0.311  38.490  -2.882  -2.566  -1.656  -0.000  -0.000  -0.000
   2_adp:  0.311  38.490  -2.882  -2.566  -1.656  -0.000  -0.000  -0.000
   2_occ:  0.311  38.490  -2.882  -2.566  -1.656  -0.000  -0.000  -0.000
   3_bss:  0.319  40.231  -2.931  -2.517  -1.382  -0.000  -0.000  -0.000
   3_xyz:  0.319  40.231  -2.931  -2.517  -1.382  -0.000  -0.000  -0.000
   3_adp:  0.319  40.231  -2.931  -2.517  -1.382  -0.000  -0.000  -0.000
   3_occ:  0.319  40.231  -2.931  -2.517  -1.382  -0.000  -0.000  -0.000
   4_bss:  0.320  40.915  -2.812  -2.396  -1.197  -0.000  -0.000  -0.000
   4_xyz:  0.320  40.915  -2.812  -2.396  -1.197  -0.000  -0.000  -0.000
   4_adp:  0.320  40.915  -2.812  -2.396  -1.197  -0.000  -0.000  -0.000
   4_occ:  0.320  40.915  -2.812  -2.396  -1.197  -0.000  -0.000  -0.000
   5_bss:  0.319  42.499  -2.632  -2.205  -1.014  -0.000  -0.000  -0.000
   5_xyz:  0.319  42.499  -2.632  -2.205  -1.014  -0.000  -0.000  -0.000
   5_adp:  0.319  42.499  -2.632  -2.205  -1.014  -0.000  -0.000  -0.000
   5_occ:  0.319  42.499  -2.632  -2.205  -1.014  -0.000  -0.000  -0.000
   5_bss:  0.318  42.483  -2.395  -1.969  -0.779  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  22.838 0.8381  1.0082    16446.480
   1_bss:  21.346 0.8512  0.9597    13218.750
   1_xyz:  13.256 0.9211  1.0006     6038.910
   1_adp:  13.756 0.9168  1.0006     6229.783
   1_occ:  13.740 0.9170  1.0004     6210.094
   2_bss:  13.617 0.9179  0.9809     6105.114
   2_xyz:  12.887 0.9238  0.9808     5665.472
   2_adp:  12.863 0.9239  0.9772     5661.076
   2_occ:  12.870 0.9239  0.9770     5656.405
   3_bss:  12.868 0.9239  0.9804     5655.572
   3_xyz:  12.886 0.9238  0.9811     5723.605
   3_adp:  12.911 0.9236  0.9764     5721.302
   3_occ:  12.920 0.9236  0.9763     5726.022
   4_bss:  12.918 0.9236  0.9814     5725.654
   4_xyz:  13.065 0.9226  0.9804     5835.067
   4_adp:  13.201 0.9216  0.9741     5888.859
   4_occ:  13.201 0.9216  0.9740     5888.178
   5_bss:  13.196 0.9216  0.9807     5884.873
   5_xyz:  13.185 0.9216  0.9810     5891.158
   5_adp:  13.237 0.9212  0.9738     5911.036
   5_occ:  13.237 0.9212  0.9737     5910.625
   5_bss:  13.240 0.9212  0.9816     5911.424
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6162e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6162e-01
   1_xyz:   0.998  0.007  0.073 15.363  0.004  4.107   6.0253e-02
   1_adp:   0.998  0.007  0.073 15.363  0.004  4.107   6.0253e-02
   1_occ:   0.998  0.007  0.073 15.363  0.004  4.107   6.0253e-02
   2_bss:   0.998  0.007  0.073 15.363  0.004  4.107   6.0253e-02
   2_xyz:   0.917  0.005  0.071 15.102  0.003  4.106   5.3215e-02
   2_adp:   0.917  0.005  0.071 15.102  0.003  4.106   5.3215e-02
   2_occ:   0.917  0.005  0.071 15.102  0.003  4.106   5.3215e-02
   3_bss:   0.917  0.005  0.071 15.102  0.003  4.106   5.3215e-02
   3_xyz:   0.992  0.007  0.076 15.239  0.004  4.118   6.1093e-02
   3_adp:   0.992  0.007  0.076 15.239  0.004  4.118   6.1093e-02
   3_occ:   0.992  0.007  0.076 15.239  0.004  4.118   6.1093e-02
   4_bss:   0.992  0.007  0.076 15.239  0.004  4.118   6.1093e-02
   4_xyz:   0.880  0.005  0.069 15.025  0.003  4.117   5.0467e-02
   4_adp:   0.880  0.005  0.069 15.025  0.003  4.117   5.0467e-02
   4_occ:   0.880  0.005  0.069 15.025  0.003  4.117   5.0467e-02
   5_bss:   0.880  0.005  0.069 15.025  0.003  4.117   5.0467e-02
   5_xyz:   0.971  0.007  0.075 15.178  0.004  4.118   5.8832e-02
   5_adp:   0.971  0.007  0.075 15.178  0.004  4.118   5.8832e-02
   5_occ:   0.971  0.007  0.075 15.178  0.004  4.118   5.8832e-02
   5_bss:   0.971  0.007  0.075 15.178  0.004  4.118   5.8832e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3951e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3951e-01
   1_xyz:   6.471  0.035  0.234 85.491  0.036  2.244   5.3110e-02
   1_adp:   6.471  0.035  0.234 85.491  0.036  2.244   5.3110e-02
   1_occ:   6.471  0.035  0.234 85.491  0.036  2.244   5.3110e-02
   2_bss:   6.471  0.035  0.234 85.491  0.036  2.244   5.3110e-02
   2_xyz:   6.225  0.038  0.217 82.354  0.031  2.367   4.1292e-02
   2_adp:   6.225  0.038  0.217 82.354  0.031  2.367   4.1292e-02
   2_occ:   6.225  0.038  0.217 82.354  0.031  2.367   4.1292e-02
   3_bss:   6.225  0.038  0.217 82.354  0.031  2.367   4.1292e-02
   3_xyz:   6.664  0.042  0.248 84.371  0.033  2.295   4.8849e-02
   3_adp:   6.664  0.042  0.248 84.371  0.033  2.295   4.8849e-02
   3_occ:   6.664  0.042  0.248 84.371  0.033  2.295   4.8849e-02
   4_bss:   6.664  0.042  0.248 84.371  0.033  2.295   4.8849e-02
   4_xyz:   5.802  0.040  0.211 83.354  0.031  2.372   2.8858e-02
   4_adp:   5.802  0.040  0.211 83.354  0.031  2.372   2.8858e-02
   4_occ:   5.802  0.040  0.211 83.354  0.031  2.372   2.8858e-02
   5_bss:   5.802  0.040  0.211 83.354  0.031  2.372   2.8858e-02
   5_xyz:   6.351  0.044  0.244 83.335  0.034  2.320   4.0842e-02
   5_adp:   6.351  0.044  0.244 83.335  0.034  2.320   4.0842e-02
   5_occ:   6.351  0.044  0.244 83.335  0.034  2.320   4.0842e-02
   5_bss:   6.351  0.044  0.244 83.335  0.034  2.320   4.0842e-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:  65.93   1.01  16.69  63.44   1.01  12.92  65.93   7.14  37.26
   1_occ:  65.93   1.01  16.69  63.44   1.01  12.92  65.93   7.14  37.26
   2_bss:  65.93   1.01  16.69  63.44   1.01  12.92  65.93   7.14  37.26
   2_xyz:  65.93   1.01  16.69  63.44   1.01  12.92  65.93   7.14  37.26
   2_adp:  68.01   2.22  16.45  66.31   2.22  12.85  68.01   5.70  36.08
   2_occ:  68.01   2.22  16.45  66.31   2.22  12.85  68.01   5.70  36.08
   3_bss:  68.01   2.22  16.45  66.31   2.22  12.85  68.01   5.70  36.08
   3_xyz:  68.01   2.22  16.45  66.31   2.22  12.85  68.01   5.70  36.08
   3_adp:  69.87   1.77  16.49  69.87   1.77  12.76  68.91   6.34  36.78
   3_occ:  69.87   1.77  16.49  69.87   1.77  12.76  68.91   6.34  36.78
   4_bss:  69.87   1.77  16.49  69.87   1.77  12.76  68.91   6.34  36.78
   4_xyz:  69.87   1.77  16.49  69.87   1.77  12.76  68.91   6.34  36.78
   4_adp:  75.93   0.90  16.66  75.93   0.90  12.72  70.77   6.36  38.07
   4_occ:  75.93   0.90  16.66  75.93   0.90  12.72  70.77   6.36  38.07
   5_bss:  75.93   0.90  16.66  75.93   0.90  12.72  70.77   6.36  38.07
   5_xyz:  75.93   0.90  16.66  75.93   0.90  12.72  70.77   6.36  38.07
   5_adp:  77.02   0.51  16.52  77.02   0.51  12.54  71.11   5.97  38.16
   5_occ:  77.02   0.51  16.52  77.02   0.51  12.54  71.11   5.97  38.16
   5_bss:  77.00   0.49  16.50  77.00   0.49  12.53  71.09   5.95  38.15
------------------------------------------------------------------------
 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:    0.576    0.009    0.215
   1_adp:    0.576    0.009    0.215
   1_occ:    0.576    0.009    0.215
   2_bss:    0.576    0.009    0.215
   2_xyz:    0.737    0.019    0.233
   2_adp:    0.737    0.019    0.233
   2_occ:    0.737    0.019    0.233
   3_bss:    0.737    0.019    0.233
   3_xyz:    0.930    0.031    0.251
   3_adp:    0.930    0.031    0.251
   3_occ:    0.930    0.031    0.251
   4_bss:    0.930    0.031    0.251
   4_xyz:    0.984    0.027    0.253
   4_adp:    0.984    0.027    0.253
   4_occ:    0.984    0.027    0.253
   5_bss:    0.984    0.027    0.253
   5_xyz:    1.050    0.025    0.257
   5_adp:    1.050    0.025    0.257
   5_occ:    1.050    0.025    0.257
   5_bss:    1.050    0.025    0.257
------------------------------------------------------------------------

CPU time actual refinement: 325.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_412/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_412/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_412/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_412/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_412/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.88 
  Macro-tasks:
    bulk solvent and scale       = 35.48  
    individual site refinement   = 138.97 
    weights calculation          = 29.03  
    collect and process          = 6.47   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 210.05 
  Micro-tasks:
    mask                            = 0.58   
    f_calc                          = 104.11 
    alpha_beta                      = 7.70   
    target                          = 1.09   
    gradients_wrt_atomic_parameters = 115.00 
    fmodel                         = 6.43   
    r_factors                      = 0.19   
    phase_errors                   = 11.22  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 246.60 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.510 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    673 calls, 103.72 s
gradients_fft:          618 calls, 100.37 s

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

# Date 2008-01-16 Time 04:45:22 PST -0800 (1200487522.31 s)
Start R-work = 0.2464, R-free = 0.2449 (no bulk solvent and anisotropic scale)
Final R-work = 0.1300, R-free = 0.1712 (no bulk solvent and anisotropic scale)

Start R-work = 0.2291, R-free = 0.2252
Final R-work = 0.1053, R-free = 0.1521