# Date 2008-01-16 Time 05:49:27 PST -0800 (1200491367.17 s)
#phil __OFF__

Command line arguments: "../896.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29499
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 896

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.99157
Completeness in resolution range: 0.968745
Completeness with d_max=infinity: 0.965784

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   1.9916

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.99157
Completeness in resolution range: 0.968745
Completeness with d_max=infinity: 0.965784

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1032 -  4.2616 [2115/2140]  1905   210   9.9%
  bin  2:  4.2616 -  3.3952 [2042/2062]  1836   206  10.1%
  bin  3:  3.3952 -  2.9697 [2018/2037]  1815   203  10.1%
  bin  4:  2.9697 -  2.6999 [2003/2033]  1810   193   9.6%
  bin  5:  2.6999 -  2.5073 [1982/2001]  1783   199  10.0%
  bin  6:  2.5073 -  2.3601 [1969/1994]  1765   204  10.4%
  bin  7:  2.3601 -  2.2423 [1948/1976]  1752   196  10.1%
  bin  8:  2.2423 -  2.1449 [1975/2011]  1778   197  10.0%
  bin  9:  2.1449 -  2.0626 [1953/1995]  1762   191   9.8%
  bin 10:  2.0626 -  1.9916 [1584/1972]  1424   160  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_896/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: 0.15 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: 9
        2.42 -     3.04: 2192
        3.04 -     3.66: 4649
        3.66 -     4.28: 9035
        4.28 -     4.90: 12302
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.239 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.239 3.040 -x+1/2,-y+1,z-1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28182 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_896/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_896/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 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: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2454   r_free= 0.2437   ksol= 0.00   Bsol= 0.00   scale= 0.998    |
|                                                                             |
| 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:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.794178                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7532 0.99   1384  154 0.2596 0.2409      6.2679      6.1906|
|  2:  4.7532 -  3.7924 0.99   1326  146 0.1910 0.1920       6.166       6.141|
|  3:  3.7924 -  3.3188 0.99   1300  143 0.1990 0.2029      6.0197      6.1517|
|  4:  3.3188 -  3.0180 0.99   1285  148 0.2118 0.2239      5.9412      5.9632|
|  5:  3.0180 -  2.8032 0.99   1292  141 0.2482 0.2357      5.8515      5.8784|
|  6:  2.8032 -  2.6388 0.99   1280  141 0.2395 0.2467      5.7556      5.7012|
|  7:  2.6388 -  2.5073 0.99   1282  138 0.2605 0.2436      5.7599      5.7994|
|  8:  2.5073 -  2.3986 0.98   1254  147 0.2564 0.2449      5.7136      5.6747|
|  9:  2.3986 -  2.3066 0.98   1270  138 0.2518 0.2634      5.6391      5.6369|
| 10:  2.3066 -  2.2273 1.00   1263  142 0.2641 0.2636      5.6521       5.623|
| 11:  2.2273 -  2.1578 0.97   1251  137 0.2802 0.2869      5.6377      5.6823|
| 12:  2.1578 -  2.0963 0.98   1254  141 0.2745 0.2582      5.5732      5.6006|
| 13:  2.0963 -  2.0413 0.99   1282  140 0.2800 0.3113      5.4888      5.4933|
| 14:  2.0413 -  1.9916 0.72    907  103 0.2906 0.2576       5.497      5.3439|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1032 -  4.7532  1384   154  0.82  23.08   0.87     0.83      33616.29|
|  2:  4.7532 -  3.7924  1326   146  0.89  16.83   0.99     0.94      28675.34|
|  3:  3.7924 -  3.3188  1300   143  0.87  19.09   1.02     1.00      24941.48|
|  4:  3.3188 -  3.0180  1285   148  0.87  19.81   1.02     0.99      20914.25|
|  5:  3.0180 -  2.8032  1292   141  0.83  23.62   1.02     0.98      17667.55|
|  6:  2.8032 -  2.6388  1280   141  0.84  23.14   1.03     0.98      14536.52|
|  7:  2.6388 -  2.5073  1282   138  0.83  23.79   1.04     0.99      13375.76|
|  8:  2.5073 -  2.3986  1254   147  0.83  23.50   1.05     1.01      12053.15|
|  9:  2.3986 -  2.3066  1270   138  0.84  23.35   1.07     1.03      11451.57|
| 10:  2.3066 -  2.2273  1263   142  0.82  24.48   1.09     1.04      11028.72|
| 11:  2.2273 -  2.1578  1251   137  0.80  26.72   1.10     1.03      11226.20|
| 12:  2.1578 -  2.0963  1254   141  0.81  25.91   1.09     1.03      10441.04|
| 13:  2.0963 -  2.0413  1282   140  0.80  27.12   1.09     1.03       8796.24|
| 14:  2.0413 -  1.9916   907   103  0.84  23.62   1.09     1.03       6316.88|
|alpha:            min =        0.83 max =            1.04 mean =         0.99|
|beta:             min =     6316.88 max =        33616.29 mean =     16458.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           90.00 mean =        23.10|
|phase err.(test): min =        0.00 max =           89.16 mean =        22.72|
|-----------------------------------------------------------------------------|

============================== 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 = 3.116186              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.383   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402147              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.600   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      198 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1994 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1832 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2817 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4661 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4374 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5621 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6681 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.136 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2454   r_free= 0.2437   ksol= 0.00   Bsol= 0.00   scale= 0.998    |
|                                                                             |
| 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:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.794178                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2290   r_free= 0.2285   ksol= 0.33   Bsol= 54.62   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.38,-2.18,-1.76,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.760569                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.828465              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.634   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.207246              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.371   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2290      final r-factor (work) = 0.1397          |
| start r-factor (free) = 0.2285      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3626 = 2.83 * 0.50 * 5.8000 + 1.00 * 0.1601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7778 = 2.83 * 0.50 * 5.4582 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1397      final r-factor (work) = 0.1287          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1373 = 0.21 * 1.00 * 5.4582 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1022 = 0.21 * 1.00 * 5.2200 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.93   16.47    None  None   None       |
|    all(noH): 2823   0      0.00    62.93   16.47    None  None   None       |
|    Sol.    : 438    0      6.85    62.93   37.13    None  None   None       |
|    Mac.    : 2385   0      0.00    52.44   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.293:  155   |   5:    31.463 -  37.755:   99        |
|      1:     6.293 -  12.585: 1336   |   6:    37.755 -  44.048:   97        |
|      2:    12.585 -  18.878:  668   |   7:    44.048 -  50.340:   74        |
|      3:    18.878 -  25.170:  204   |   8:    50.340 -  56.633:   60        |
|      4:    25.170 -  31.463:  109   |   9:    56.633 -  62.925:   21        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1287 r_free = 0.1610             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1609             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1609   ksol= 0.33   Bsol= 54.62   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.38,-2.18,-1.76,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.225910                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1600   ksol= 0.33   Bsol= 54.62   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.77,-1.77,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.225936                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.687913              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.311  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.159064              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.780   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0804 = 2.69 * 0.50 * 5.2247 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0075 = 2.69 * 0.50 * 5.1643 + 1.00 * 0.0669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1509          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8674 = 0.16 * 1.00 * 5.1643 + 1.00 * 0.0459                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8215 = 0.16 * 1.00 * 5.1229 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.13    65.73   16.57    None  None   None       |
|    all(noH): 2823   0      2.13    65.73   16.57    None  None   None       |
|    Sol.    : 438    0      5.79    65.73   36.86    None  None   None       |
|    Mac.    : 2385   0      2.13    65.34   12.84    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:     2.128 -   8.488:  553   |   5:    33.927 -  40.287:  115        |
|      1:     8.488 -  14.848: 1296   |   6:    40.287 -  46.647:   82        |
|      2:    14.848 -  21.208:  394   |   7:    46.647 -  53.007:   91        |
|      3:    21.208 -  27.567:  144   |   8:    53.007 -  59.367:   37        |
|      4:    27.567 -  33.927:  101   |   9:    59.367 -  65.727:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1509             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1510             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1510   ksol= 0.33   Bsol= 54.62   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.77,-1.77,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118203                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1510   ksol= 0.33   Bsol= 54.62   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.64,-1.51,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118036                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.534925              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.083  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.399027              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.902  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1510      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9987 = 1.53 * 0.50 * 5.1231 + 1.00 * 0.0669                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9876 = 1.53 * 0.50 * 5.1244 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0514 = 0.40 * 1.00 * 5.1244 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0525 = 0.40 * 1.00 * 5.1239 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    73.73   16.81    None  None   None       |
|    all(noH): 2823   0      1.26    73.73   16.81    None  None   None       |
|    Sol.    : 438    0      6.44    69.29   38.31    None  None   None       |
|    Mac.    : 2385   0      1.26    73.73   12.86    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:     1.259 -   8.506:  621   |   5:    37.495 -  44.742:  115        |
|      1:     8.506 -  15.754: 1308   |   6:    44.742 -  51.989:   86        |
|      2:    15.754 -  23.001:  360   |   7:    51.989 -  59.236:   67        |
|      3:    23.001 -  30.248:  128   |   8:    59.236 -  66.483:   26        |
|      4:    30.248 -  37.495:  106   |   9:    66.483 -  73.730:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1533             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1534             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1534   ksol= 0.33   Bsol= 54.62   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.64,-1.51,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1533   ksol= 0.33   Bsol= 54.62   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.50,-1.33,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127261                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.739488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.258  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.295087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.836  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0736 = 2.74 * 0.50 * 5.1242 + 1.00 * 0.0548                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0700 = 2.74 * 0.50 * 5.1115 + 1.00 * 0.0686                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1067      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5163 = 0.30 * 1.00 * 5.1115 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5153 = 0.30 * 1.00 * 5.1084 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.27    75.19   16.62    None  None   None       |
|    all(noH): 2823   0      1.27    75.19   16.62    None  None   None       |
|    Sol.    : 438    0      6.49    70.44   37.99    None  None   None       |
|    Mac.    : 2385   0      1.27    75.19   12.70    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:     1.272 -   8.664:  703   |   5:    38.232 -  45.624:  105        |
|      1:     8.664 -  16.056: 1251   |   6:    45.624 -  53.016:   84        |
|      2:    16.056 -  23.448:  359   |   7:    53.016 -  60.408:   58        |
|      3:    23.448 -  30.840:  121   |   8:    60.408 -  67.800:   23        |
|      4:    30.840 -  38.232:  113   |   9:    67.800 -  75.192:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1532             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1067 r_free = 0.1533             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1533   ksol= 0.33   Bsol= 54.62   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.50,-1.33,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.107546                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1534   ksol= 0.33   Bsol= 54.62   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.30,-1.10,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.107643                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.330118              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 168.369  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.520290              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.908  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0212 = 2.33 * 0.50 * 5.1095 + 1.00 * 0.0684                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0171 = 2.33 * 0.50 * 5.1110 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6671 = 0.52 * 1.00 * 5.1110 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6693 = 0.52 * 1.00 * 5.1144 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    76.06   16.50    None  None   None       |
|    all(noH): 2823   0      0.81    76.06   16.50    None  None   None       |
|    Sol.    : 438    0      6.10    70.81   38.07    None  None   None       |
|    Mac.    : 2385   0      0.81    76.06   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:     0.814 -   8.338:  685   |   5:    38.436 -  45.960:  105        |
|      1:     8.338 -  15.863: 1264   |   6:    45.960 -  53.485:   87        |
|      2:    15.863 -  23.387:  359   |   7:    53.485 -  61.009:   56        |
|      3:    23.387 -  30.912:  127   |   8:    61.009 -  68.534:   23        |
|      4:    30.912 -  38.436:  111   |   9:    68.534 -  76.058:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1551             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1551             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1551   ksol= 0.33   Bsol= 54.62   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.30,-1.10,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117517                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7532 0.99   1384  154 0.0997 0.1287      5.3972      5.5404|
|  2:  4.7532 -  3.7924 0.99   1326  146 0.0857 0.1137      5.4442      5.6304|
|  3:  3.7924 -  3.3188 0.99   1300  143 0.1031 0.1493      5.4611      5.8571|
|  4:  3.3188 -  3.0180 0.99   1285  148 0.1168 0.1551      5.4341      5.5699|
|  5:  3.0180 -  2.8032 0.99   1292  141 0.1271 0.1756      5.3059      5.5698|
|  6:  2.8032 -  2.6388 0.99   1280  141 0.1150 0.1843      5.1893      5.4446|
|  7:  2.6388 -  2.5073 0.99   1282  138 0.1219 0.1476      5.1407      5.3153|
|  8:  2.5073 -  2.3986 0.98   1254  147 0.1085 0.1707      5.0114      5.3235|
|  9:  2.3986 -  2.3066 0.98   1270  138 0.1087 0.1621      4.9853      5.2223|
| 10:  2.3066 -  2.2273 1.00   1263  142 0.1041 0.1731      4.9167      5.2675|
| 11:  2.2273 -  2.1578 0.97   1251  137 0.1080 0.1626      4.9194      5.1821|
| 12:  2.1578 -  2.0963 0.98   1254  141 0.1043 0.1680      4.8469      5.1873|
| 13:  2.0963 -  2.0413 0.99   1282  140 0.1045 0.1743      4.7555      5.0742|
| 14:  2.0413 -  1.9916 0.72    907  103 0.0999 0.1677      4.6401      4.9013|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1032 -  4.7532  1384   154  0.94   9.35   0.98     0.95       7419.61|
|  2:  4.7532 -  3.7924  1326   146  0.95   7.95   1.01     0.99       9240.27|
|  3:  3.7924 -  3.3188  1300   143  0.94  11.07   1.02     1.01      10215.06|
|  4:  3.3188 -  3.0180  1285   148  0.92  13.40   1.00     0.98      10088.47|
|  5:  3.0180 -  2.8032  1292   141  0.90  15.67   0.99     0.96       8150.70|
|  6:  2.8032 -  2.6388  1280   141  0.90  15.54   0.98     0.96       6962.15|
|  7:  2.6388 -  2.5073  1282   138  0.91  15.20   0.99     0.96       5950.18|
|  8:  2.5073 -  2.3986  1254   147  0.92  14.15   0.98     0.96       4722.56|
|  9:  2.3986 -  2.3066  1270   138  0.92  14.40   0.99     0.96       4566.21|
| 10:  2.3066 -  2.2273  1263   142  0.91  14.61   0.99     0.95       4063.34|
| 11:  2.2273 -  2.1578  1251   137  0.90  16.25   0.99     0.95       4283.93|
| 12:  2.1578 -  2.0963  1254   141  0.92  14.38   1.00     0.98       3768.17|
| 13:  2.0963 -  2.0413  1282   140  0.91  15.43   0.99     0.98       3212.85|
| 14:  2.0413 -  1.9916   907   103  0.92  14.07   0.97     0.93       2461.03|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2461.03 max =        10215.06 mean =      6189.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.62|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1551   ksol= 0.33   Bsol= 54.59   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.10,-0.90,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.117606                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1551   ksol= 0.33   Bsol= 54.59   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.10,-0.90,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.117606                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7532 0.99   1384  154 0.0997 0.1289      5.3978      5.5413|
|  2:  4.7532 -  3.7924 0.99   1326  146 0.0857 0.1136      5.4445      5.6302|
|  3:  3.7924 -  3.3188 0.99   1300  143 0.1031 0.1493       5.461      5.8572|
|  4:  3.3188 -  3.0180 0.99   1285  148 0.1168 0.1552      5.4341      5.5699|
|  5:  3.0180 -  2.8032 0.99   1292  141 0.1271 0.1756      5.3059      5.5696|
|  6:  2.8032 -  2.6388 0.99   1280  141 0.1150 0.1843      5.1893      5.4445|
|  7:  2.6388 -  2.5073 0.99   1282  138 0.1219 0.1476      5.1408      5.3155|
|  8:  2.5073 -  2.3986 0.98   1254  147 0.1085 0.1707      5.0114      5.3234|
|  9:  2.3986 -  2.3066 0.98   1270  138 0.1087 0.1621      4.9854      5.2224|
| 10:  2.3066 -  2.2273 1.00   1263  142 0.1041 0.1731      4.9169      5.2674|
| 11:  2.2273 -  2.1578 0.97   1251  137 0.1080 0.1626      4.9195      5.1821|
| 12:  2.1578 -  2.0963 0.98   1254  141 0.1043 0.1680      4.8469      5.1874|
| 13:  2.0963 -  2.0413 0.99   1282  140 0.1045 0.1743      4.7555       5.074|
| 14:  2.0413 -  1.9916 0.72    907  103 0.0999 0.1677      4.6401      4.9013|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1032 -  4.7532  1384   154  0.94   9.36   0.98     0.95       7431.98|
|  2:  4.7532 -  3.7924  1326   146  0.95   7.95   1.01     1.00       9246.61|
|  3:  3.7924 -  3.3188  1300   143  0.94  11.07   1.02     1.02      10212.54|
|  4:  3.3188 -  3.0180  1285   148  0.92  13.40   1.01     0.99      10087.83|
|  5:  3.0180 -  2.8032  1292   141  0.90  15.67   0.99     0.96       8149.82|
|  6:  2.8032 -  2.6388  1280   141  0.90  15.54   0.99     0.96       6961.57|
|  7:  2.6388 -  2.5073  1282   138  0.91  15.20   0.99     0.96       5949.78|
|  8:  2.5073 -  2.3986  1254   147  0.92  14.15   0.99     0.97       4722.32|
|  9:  2.3986 -  2.3066  1270   138  0.92  14.40   1.00     0.97       4566.19|
| 10:  2.3066 -  2.2273  1263   142  0.91  14.62   1.00     0.96       4064.27|
| 11:  2.2273 -  2.1578  1251   137  0.90  16.25   1.00     0.96       4284.57|
| 12:  2.1578 -  2.0963  1254   141  0.92  14.38   1.01     0.99       3768.29|
| 13:  2.0963 -  2.0413  1282   140  0.91  15.43   1.00     0.99       3212.62|
| 14:  2.0413 -  1.9916   907   103  0.92  14.07   0.98     0.94       2461.21|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2461.21 max =        10212.54 mean =      6190.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.62|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    76.03   16.47    None  None   None       |
|    all(noH): 2823   0      0.79    76.03   16.47    None  None   None       |
|    Sol.    : 438    0      6.08    70.78   38.05    None  None   None       |
|    Mac.    : 2385   0      0.79    76.03   12.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.786 -   8.311:  685   |   5:    38.408 -  45.933:  105        |
|      1:     8.311 -  15.835: 1264   |   6:    45.933 -  53.457:   87        |
|      2:    15.835 -  23.360:  359   |   7:    53.457 -  60.982:   56        |
|      3:    23.360 -  30.884:  127   |   8:    60.982 -  68.506:   23        |
|      4:    30.884 -  38.408:  111   |   9:    68.506 -  76.031:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 285         
Filter by distance & map next to the model:
   mapped sites are within: 0.499 - 4.745
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 279 from: 285
   mapped sites are within: 0.703 - 4.745

peak=    5.992 closest distance to " NH2 ARG A  56 " =    2.221
peak=    5.686 closest distance to " CG  PRO A  54 " =    1.316
peak=    5.382 closest distance to " O   HOH Z 126 " =    1.945
peak=    5.168 closest distance to " CB  SER A  63 " =    1.202
peak=    5.137 closest distance to " CB  GLN A 223 " =    1.432
peak=    4.955 closest distance to " CB  ARG A 275 " =    0.905
peak=    4.945 closest distance to " NE2 GLN A  11 " =    1.121
peak=    4.865 closest distance to " O   HOH Z 232 " =    2.359
peak=    4.756 closest distance to " O   HOH Z 144 " =    1.720
peak=    4.706 closest distance to " O   HOH Z  78 " =    1.759
peak=    4.633 closest distance to " CB  GLN A 183 " =    1.208
peak=    4.606 closest distance to " CB  PRO A  54 " =    0.946
peak=    4.600 closest distance to " CB  ARG A  79 " =    1.312
peak=    4.571 closest distance to " O   HOH Z 369 " =    2.107
peak=    4.505 closest distance to " O   HOH Z  15 " =    2.263
peak=    4.504 closest distance to " O   HOH Z 236 " =    2.012
peak=    4.478 closest distance to " CA  TYR A  30 " =    0.945
peak=    4.477 closest distance to " O   HOH Z 298 " =    1.938
peak=    4.464 closest distance to " C   PRO A 198 " =    1.489
peak=    4.428 closest distance to " CB  LEU A 228 " =    1.081
peak=    4.421 closest distance to " CB  GLU A 152 " =    1.211
peak=    4.399 closest distance to " CB  ASN A 148 " =    1.486
peak=    4.346 closest distance to " CG  PRO A 198 " =    1.266
peak=    4.298 closest distance to " OD1 ASN A  69 " =    2.607
peak=    4.268 closest distance to " CB  ARG A 190 " =    1.580
peak=    4.266 closest distance to " O   HOH Z 427 " =    2.932
peak=    4.265 closest distance to " O   HOH Z 250 " =    1.564
peak=    4.238 closest distance to " ND2 ASN A 187 " =    1.475
peak=    4.237 closest distance to " CG2 VAL A 257 " =    0.940
peak=    4.205 closest distance to " CB  TYR A 169 " =    0.715
peak=    4.193 closest distance to " O   HOH Z 234 " =    3.748
peak=    4.151 closest distance to " CA  ASN A 215 " =    1.219
peak=    4.149 closest distance to " O   HOH Z 193 " =    1.904
peak=    4.144 closest distance to " O   HOH Z 189 " =    2.444
peak=    4.144 closest distance to " O   HOH Z  78 " =    2.145
peak=    4.140 closest distance to " O   HOH Z 158 " =    3.023
peak=    4.134 closest distance to " O   HOH Z 303 " =    2.106
peak=    4.083 closest distance to " CG  PRO A 243 " =    1.047
peak=    4.076 closest distance to " O   HOH Z 316 " =    3.123
peak=    4.074 closest distance to " O   HOH Z 272 " =    1.853
peak=    4.035 closest distance to " CB  GLU A 128 " =    1.042
peak=    4.013 closest distance to " CB  ASN A 187 " =    1.060
peak=    3.980 closest distance to " CB  TRP A 266 " =    0.975
peak=    3.979 closest distance to " NZ  LYS A 117 " =    3.234
peak=    3.978 closest distance to " O   HOH Z 346 " =    1.627
peak=    3.959 closest distance to " CZ  PHE A 218 " =    1.034
peak=    3.946 closest distance to " O   HOH Z  54 " =    2.500
peak=    3.943 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.932 closest distance to " O   HOH Z 261 " =    2.083
peak=    3.931 closest distance to " O   HOH Z 386 " =    3.200
peak=    3.908 closest distance to " CB  ASP A 140 " =    0.950
peak=    3.897 closest distance to " CD  ARG A 159 " =    0.745
peak=    3.879 closest distance to " O   HOH Z  61 " =    1.574
peak=    3.867 closest distance to " O   HOH Z 209 " =    2.337
peak=    3.861 closest distance to " O   HOH Z   1 " =    1.962
peak=    3.859 closest distance to " O   HOH Z 203 " =    1.814
peak=    3.848 closest distance to " CB  SER A   3 " =    1.323
peak=    3.846 closest distance to " O   HOH Z 214 " =    2.041
peak=    3.846 closest distance to " CB  VAL A 265 " =    1.246
peak=    3.842 closest distance to " NH1AARG A 145 " =    1.212
peak=    3.796 closest distance to " CD2 TRP A 179 " =    1.325
peak=    3.792 closest distance to " CB  SER A 212 " =    1.141
peak=    3.790 closest distance to " O   HOH Z 193 " =    1.700
peak=    3.789 closest distance to " CD  ARG A  66 " =    2.369
peak=    3.787 closest distance to " O   HOH Z 426 " =    1.837
peak=    3.781 closest distance to " O   HOH Z  66 " =    2.188
peak=    3.773 closest distance to " CB  SER A 216 " =    0.840
peak=    3.765 closest distance to " CB  TYR A 169 " =    0.703
peak=    3.763 closest distance to " O   HOH Z  10 " =    1.841
peak=    3.760 closest distance to " CD1 LEU A 300 " =    1.243
peak=    3.755 closest distance to " O   HOH Z 245 " =    1.276
peak=    3.754 closest distance to " OD2 ASP A 286 " =    2.867
peak=    3.751 closest distance to " O   HOH Z 344 " =    3.165
peak=    3.750 closest distance to " O   HOH Z   9 " =    2.031
peak=    3.744 closest distance to " O   SER A  87 " =    2.263
peak=    3.730 closest distance to " CG1 ILE A  33 " =    1.233
peak=    3.726 closest distance to " O   HOH Z 389 " =    1.936
peak=    3.725 closest distance to " CA  ALA A  51 " =    0.922
peak=    3.716 closest distance to " O   HOH Z 368 " =    2.058
peak=    3.710 closest distance to " O   HOH Z  40 " =    1.815
peak=    3.708 closest distance to " CA  THR A 264 " =    0.870
peak=    3.696 closest distance to " O   HOH Z 291 " =    1.548
peak=    3.689 closest distance to " O   HOH Z 219 " =    2.043
peak=    3.680 closest distance to " CB  VAL A 202 " =    1.594
peak=    3.665 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.653 closest distance to " CD2 LEU A 255 " =    1.507
peak=    3.652 closest distance to " O   HOH Z 280 " =    2.984
peak=    3.651 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.651 closest distance to " O   HOH Z 132 " =    2.579
peak=    3.644 closest distance to " O   HOH Z 180 " =    2.159
peak=    3.643 closest distance to " CB  ASN A  39 " =    0.919
peak=    3.628 closest distance to " CD BLYS A 290 " =    1.079
peak=    3.623 closest distance to " O   HOH Z  21 " =    1.753
peak=    3.621 closest distance to " CG1BVAL A  72 " =    1.652
peak=    3.618 closest distance to " CB  GLU A 277 " =    3.592
peak=    3.614 closest distance to " CB  TRP A 179 " =    1.365
peak=    3.612 closest distance to " O   HOH Z 419 " =    2.007
peak=    3.610 closest distance to " O   HOH Z 248 " =    1.647
peak=    3.608 closest distance to " CB  ALA A 291 " =    1.375
peak=    3.606 closest distance to " O   HOH Z 425 " =    2.169
peak=    3.592 closest distance to " O   HOH Z 305 " =    3.549
peak=    3.591 closest distance to " ND1 HIS A  86 " =    1.710
peak=    3.590 closest distance to " O   HOH Z 133 " =    1.626
peak=    3.585 closest distance to " N   ARG A 156 " =    1.305
peak=    3.585 closest distance to " O   HOH Z 403 " =    1.667
peak=    3.585 closest distance to " O   HOH Z 313 " =    1.969
peak=    3.569 closest distance to " O   HOH Z 213 " =    1.843
peak=    3.563 closest distance to " CB  ASN A 142 " =    0.981
peak=    3.558 closest distance to " CB  ALA A  34 " =    0.954
peak=    3.552 closest distance to " CA  SER A  87 " =    1.024
peak=    3.545 closest distance to " O   HOH Z 133 " =    2.425
peak=    3.545 closest distance to " O   HOH Z 172 " =    3.222
peak=    3.545 closest distance to " CB  GLN A  88 " =    1.250
peak=    3.545 closest distance to " CG2 THR A 221 " =    1.075
peak=    3.543 closest distance to " O   HOH Z 371 " =    3.048
peak=    3.542 closest distance to " CB  GLU A  46 " =    1.000
peak=    3.534 closest distance to " CA  ALA A  21 " =    1.158
peak=    3.528 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.525 closest distance to " O   HOH Z  53 " =    2.574
peak=    3.517 closest distance to " CA  THR A 221 " =    1.000
peak=    3.495 closest distance to " CB  MET A  47 " =    1.034
peak=    3.486 closest distance to " O   HOH Z 273 " =    2.801
peak=    3.479 closest distance to " CB  ARG A 139 " =    0.948
peak=    3.470 closest distance to " O   HOH Z 135 " =    1.646
peak=    3.463 closest distance to " O   MET A 105 " =    1.823
peak=    3.463 closest distance to " CB  ASN A 224 " =    1.012
peak=    3.462 closest distance to " CB  TYR A 116 " =    0.802
peak=    3.460 closest distance to " O   HOH Z  59 " =    1.869
peak=    3.459 closest distance to " CB  LEU A 143 " =    1.119
peak=    3.457 closest distance to " CA  ARG A  36 " =    1.062
peak=    3.452 closest distance to " O   HOH Z  61 " =    1.484
peak=    3.449 closest distance to " N   ASN A 127 " =    1.256
peak=    3.448 closest distance to " O   HOH Z  88 " =    3.273
peak=    3.447 closest distance to " CD1 ILE A 106 " =    0.758
peak=    3.446 closest distance to " CB  MET A  40 " =    0.802
peak=    3.444 closest distance to " NH2BARG A 145 " =    2.112
peak=    3.442 closest distance to " CA  MET A  40 " =    1.121
peak=    3.442 closest distance to " OG  SER A  22 " =    2.740
peak=    3.442 closest distance to " CG2 ILE A 120 " =    1.156
peak=    3.441 closest distance to " NE2 GLN A  73 " =    3.826
peak=    3.441 closest distance to " NH2 ARG A 156 " =    1.230
peak=    3.440 closest distance to " O   HOH Z 402 " =    1.352
peak=    3.436 closest distance to " O   HOH Z 147 " =    1.800
peak=    3.429 closest distance to " O  BHOH Z 338 " =    2.367
peak=    3.428 closest distance to " ND2 ASN A 110 " =    1.728
peak=    3.420 closest distance to " CB  THR A 157 " =    1.119
peak=    3.416 closest distance to " O   HOH Z 175 " =    2.220
peak=    3.416 closest distance to " O   HOH Z 285 " =    2.815
peak=    3.410 closest distance to " O   HOH Z 371 " =    1.859
peak=    3.402 closest distance to " O   HOH Z 128 " =    2.325
peak=    3.397 closest distance to " CD2 LEU A 297 " =    0.858
peak=    3.397 closest distance to " CA  ALA A 158 " =    1.252
peak=    3.395 closest distance to " O   HOH Z 234 " =    1.765
peak=    3.390 closest distance to " O   HOH Z 132 " =    3.145
peak=    3.388 closest distance to " O   HOH Z 148 " =    3.339
peak=    3.386 closest distance to " O   HOH Z  96 " =    1.975
peak=    3.386 closest distance to " CG1 VAL A 153 " =    0.901
peak=    3.384 closest distance to " O   HOH Z 417 " =    3.213
peak=    3.378 closest distance to " CB  ASN A 110 " =    1.104
peak=    3.374 closest distance to " O   HOH Z 345 " =    3.525
peak=    3.373 closest distance to " OG BSER A 164 " =    2.319
peak=    3.372 closest distance to " O   HOH Z 423 " =    1.762
peak=    3.368 closest distance to " CA  ALA A 233 " =    1.259
peak=    3.355 closest distance to " O   HOH Z  64 " =    2.056
peak=    3.354 closest distance to " CD  LYS A 166 " =    1.227
peak=    3.353 closest distance to " CB  ILE A 120 " =    1.238
peak=    3.351 closest distance to " NH2AARG A 275 " =    3.690
peak=    3.348 closest distance to " CB  ALA A 233 " =    1.348
peak=    3.347 closest distance to " CB  HIS A 108 " =    0.779
peak=    3.346 closest distance to " OD1BASN A 224 " =    2.379
peak=    3.345 closest distance to " CB  GLN A  89 " =    1.322
peak=    3.342 closest distance to " O   HOH Z 185 " =    1.801
peak=    3.332 closest distance to " O   HOH Z 213 " =    2.232
peak=    3.331 closest distance to " O   THR A 251 " =    1.261
peak=    3.329 closest distance to " O   HOH Z 411 " =    3.850
peak=    3.328 closest distance to " OG  SER A  97 " =    3.674
peak=    3.327 closest distance to " O   HOH Z 188 " =    2.077
peak=    3.319 closest distance to " O   HOH Z 294 " =    1.515
peak=    3.318 closest distance to " O   HOH Z  44 " =    3.059
peak=    3.315 closest distance to " CD  ARG A 219 " =    1.136
peak=    3.315 closest distance to " CB  THR A 235 " =    1.054
peak=    3.312 closest distance to " CD2 HIS A  81 " =    1.104
peak=    3.309 closest distance to " O   HOH Z   1 " =    1.742
peak=    3.307 closest distance to " CB  ALA A 242 " =    0.885
peak=    3.306 closest distance to " O   HOH Z  43 " =    1.996
peak=    3.304 closest distance to " OG  SER A 206 " =    1.230
peak=    3.304 closest distance to " OE1 GLU A   2 " =    2.158
peak=    3.303 closest distance to " CD  ARG A 269 " =    0.929
peak=    3.301 closest distance to " CE1 TYR A 186 " =    1.356
peak=    3.301 closest distance to " CG1 VAL A 189 " =    2.064
peak=    3.300 closest distance to " OG1 THR A 294 " =    2.410
peak=    3.298 closest distance to " O   HOH Z 409 " =    2.804
peak=    3.296 closest distance to " O   HOH Z 353 " =    2.719
peak=    3.296 closest distance to " O   HOH Z 437 " =    1.359
peak=    3.294 closest distance to " N   PHE A 130 " =    1.225
peak=    3.294 closest distance to " O   HOH Z 391 " =    2.866
peak=    3.290 closest distance to " NE2 HIS A 207 " =    1.364
peak=    3.278 closest distance to " CA  ALA A  84 " =    1.354
peak=    3.277 closest distance to " CB  ALA A   9 " =    1.540
peak=    3.272 closest distance to " CB  SER A 141 " =    1.031
peak=    3.271 closest distance to " O   HOH Z 407 " =    2.327
peak=    3.268 closest distance to " CB  ALA A 248 " =    1.293
peak=    3.266 closest distance to " O   HOH Z 261 " =    2.301
peak=    3.266 closest distance to " CB  ALA A 248 " =    0.887
peak=    3.263 closest distance to " CB  ALA A   1 " =    4.745
peak=    3.263 closest distance to " O   ALA A 165 " =    1.522
peak=    3.262 closest distance to " O   HOH Z 128 " =    2.213
peak=    3.260 closest distance to " O   HOH Z 329 " =    3.848
peak=    3.251 closest distance to " CA  ALA A 248 " =    1.188
peak=    3.251 closest distance to " O   HOH Z 193 " =    2.016
peak=    3.248 closest distance to " O   HOH Z 327 " =    1.811
peak=    3.248 closest distance to " O   THR A 220 " =    1.259
peak=    3.247 closest distance to " O   HOH Z 171 " =    2.029
peak=    3.245 closest distance to " CG  LYS A  76 " =    0.981
peak=    3.238 closest distance to " CD1 LEU A  96 " =    0.790
peak=    3.236 closest distance to " N   ASN A  39 " =    1.266
peak=    3.234 closest distance to " CZ2 TRP A 179 " =    1.754
peak=    3.232 closest distance to " CA  LYS A 117 " =    1.213
peak=    3.231 closest distance to " CA  ALA A 154 " =    0.984
peak=    3.222 closest distance to " CA  MET A 105 " =    0.974
peak=    3.221 closest distance to " CA  ALA A 291 " =    0.866
peak=    3.221 closest distance to " O   HOH Z 435 " =    1.930
peak=    3.217 closest distance to " CG  ARG A 159 " =    0.864
peak=    3.215 closest distance to " NZ  LYS A  76 " =    1.538
peak=    3.210 closest distance to " N   GLN A 278 " =    1.160
peak=    3.203 closest distance to " CA  ASN A 217 " =    1.229
peak=    3.196 closest distance to " CB  TRP A 150 " =    1.304
peak=    3.196 closest distance to " O   HOH Z 411 " =    1.757
peak=    3.195 closest distance to " O   HOH Z 423 " =    2.829
peak=    3.195 closest distance to " O   HOH Z 295 " =    1.530
peak=    3.188 closest distance to " CB  ARG A 138 " =    0.989
peak=    3.188 closest distance to " N   VAL A 126 " =    1.328
peak=    3.186 closest distance to " CG  GLN A  89 " =    1.489
peak=    3.185 closest distance to " CG  GLN A  77 " =    2.234
peak=    3.185 closest distance to " O   HOH Z  49 " =    2.808
peak=    3.184 closest distance to " O   HOH Z  93 " =    2.712
peak=    3.180 closest distance to " O   HOH Z  40 " =    1.955
peak=    3.175 closest distance to " O   HOH Z 406 " =    1.557
peak=    3.173 closest distance to " CA  TYR A 116 " =    1.340
peak=    3.169 closest distance to " CD1 ILE A 263 " =    1.322
peak=    3.166 closest distance to " ND1 HIS A  81 " =    1.658
peak=    3.166 closest distance to " CG  PRO A 213 " =    0.959
peak=    3.165 closest distance to " O   HOH Z 383 " =    1.809
peak=    3.163 closest distance to " CB  VAL A 268 " =    0.866
peak=    3.155 closest distance to " O   HOH Z 359 " =    1.420
peak=    3.141 closest distance to " ND2 ASN A 249 " =    0.891
peak=    3.140 closest distance to " CA  SER A 146 " =    1.685
peak=    3.139 closest distance to " CB  PRO A  90 " =    1.236
peak=    3.135 closest distance to " CB  SER A 273 " =    0.849
peak=    3.133 closest distance to " NH1 ARG A 138 " =    1.069
peak=    3.131 closest distance to " CA  GLU A  46 " =    0.730
peak=    3.122 closest distance to " O   HOH Z 271 " =    2.536
peak=    3.119 closest distance to " CD  LYS A 119 " =    1.296
peak=    3.118 closest distance to " O   HOH Z 171 " =    4.038
peak=    3.117 closest distance to " CB  LYS A 117 " =    1.191
peak=    3.112 closest distance to " CG  GLN A 278 " =    1.235
peak=    3.110 closest distance to " O   HOH Z 298 " =    2.555
peak=    3.105 closest distance to " O   HOH Z  97 " =    2.032
peak=    3.105 closest distance to " O   HOH Z 302 " =    1.941
peak=    3.103 closest distance to " O   HOH Z 116 " =    1.768
peak=    3.100 closest distance to " O   TYR A 116 " =    1.287
peak=    3.094 closest distance to " O   HOH Z 201 " =    3.231
peak=    3.094 closest distance to " CA  ARG A 102 " =    1.061
peak=    3.092 closest distance to " CB  GLN A 278 " =    0.837
peak=    3.091 closest distance to " CB  SER A  62 " =    1.152
peak=    3.089 closest distance to " CB  LEU A 255 " =    0.759
peak=    3.088 closest distance to " O   ALA A   1 " =    1.680
peak=    3.082 closest distance to " CB  VAL A 126 " =    0.998
peak=    3.078 closest distance to " N   SER A 135 " =    1.280
peak=    3.075 closest distance to " O   HOH Z  49 " =    2.180
peak=    3.073 closest distance to " O   HOH Z 287 " =    2.287
peak=    3.060 closest distance to " CB  ALA A 114 " =    0.819
peak=    3.060 closest distance to " O   TRP A 274 " =    1.816
peak=    3.058 closest distance to " O   HOH Z  88 " =    2.007
peak=    3.055 closest distance to " O   HOH Z 357 " =    1.890
peak=    3.050 closest distance to " CB  ASN A 215 " =    1.101
peak=    3.038 closest distance to " CB  VAL A 265 " =    1.964
peak=    3.033 closest distance to " O   ALA A 158 " =    1.307
peak=    3.017 closest distance to " O   HOH Z 438 " =    2.942

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.785 - 5.413
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.785 - 5.413

peak=   -4.590 closest distance to " CB  PRO A 243 " =    2.607
peak=   -4.574 closest distance to " CD  ARG A 156 " =    1.995
peak=   -4.572 closest distance to " O   HOH Z 266 " =    5.054
peak=   -4.391 closest distance to " O   VAL A  67 " =    2.725
peak=   -4.385 closest distance to " CG1 VAL A 112 " =    2.630
peak=   -4.331 closest distance to " CG  GLN A 223 " =    1.878
peak=   -4.325 closest distance to " O   HOH Z 389 " =    1.951
peak=   -4.266 closest distance to " SG  CYS A 254 " =    3.545
peak=   -4.161 closest distance to " CD  GLN A  58 " =    0.962
peak=   -4.142 closest distance to " O   HOH Z 435 " =    2.805
peak=   -4.123 closest distance to " CZ3 TRP A 179 " =    1.130
peak=   -4.123 closest distance to " OG BSER A 134 " =    1.219
peak=   -4.093 closest distance to " O   HOH Z 377 " =    2.056
peak=   -4.079 closest distance to " C   HIS A 108 " =    1.068
peak=   -4.040 closest distance to " O   HOH Z 231 " =    2.209
peak=   -4.021 closest distance to " O   HOH Z 198 " =    2.084
peak=   -3.984 closest distance to " CG1 VAL A 112 " =    2.880
peak=   -3.955 closest distance to " ND2 ASN A  45 " =    1.819
peak=   -3.914 closest distance to " O   HOH Z 372 " =    2.399
peak=   -3.893 closest distance to " N   ALA A  43 " =    2.627
peak=   -3.886 closest distance to " O   HOH Z 290 " =    1.186
peak=   -3.879 closest distance to " CD1 PHE A  59 " =    1.848
peak=   -3.874 closest distance to " CD  ARG A 139 " =    1.532
peak=   -3.859 closest distance to " CG2 ILE A 263 " =    2.347
peak=   -3.857 closest distance to " O   HOH Z  43 " =    1.601
peak=   -3.852 closest distance to " O   PRO A 198 " =    1.310
peak=   -3.851 closest distance to " CB  ALA A 291 " =    2.231
peak=   -3.849 closest distance to " CE  MET A 105 " =    2.332
peak=   -3.834 closest distance to " O   HOH Z  10 " =    1.540
peak=   -3.826 closest distance to " O   HOH Z 313 " =    1.937
peak=   -3.795 closest distance to " CG  PHE A 283 " =    2.717
peak=   -3.789 closest distance to " CZ  PHE A  59 " =    1.547
peak=   -3.782 closest distance to " O   ILE A 109 " =    2.578
peak=   -3.757 closest distance to " O   HOH Z 351 " =    1.491
peak=   -3.751 closest distance to " O   VAL A  67 " =    2.867
peak=   -3.749 closest distance to " O   HOH Z 198 " =    1.367
peak=   -3.739 closest distance to " OD1 ASP A 171 " =    1.611
peak=   -3.736 closest distance to " O   HOH Z 353 " =    2.165
peak=   -3.726 closest distance to " CD2 PHE A 192 " =    2.044
peak=   -3.721 closest distance to " O   HOH Z 407 " =    3.208
peak=   -3.710 closest distance to " CB  ALA A  43 " =    2.556
peak=   -3.703 closest distance to " CB  ASN A  39 " =    2.314
peak=   -3.696 closest distance to " O   HOH Z 185 " =    2.253
peak=   -3.693 closest distance to " CB  ALA A 291 " =    2.412
peak=   -3.685 closest distance to " O   HOH Z 311 " =    3.692
peak=   -3.682 closest distance to " NH2AARG A 275 " =    5.413
peak=   -3.681 closest distance to " N   ASP A 286 " =    2.458
peak=   -3.679 closest distance to " O   HOH Z 196 " =    2.096
peak=   -3.671 closest distance to " O   HOH Z 114 " =    3.138
peak=   -3.665 closest distance to " CE2 TYR A  30 " =    2.796
peak=   -3.655 closest distance to " O   HOH Z 211 " =    1.677
peak=   -3.642 closest distance to " CA  GLY A 203 " =    2.338
peak=   -3.634 closest distance to " O   HOH Z 126 " =    1.915
peak=   -3.632 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.623 closest distance to " OG  SER A  97 " =    2.206
peak=   -3.619 closest distance to " O   VAL A 189 " =    2.595
peak=   -3.606 closest distance to " CD2 PHE A  61 " =    2.520
peak=   -3.592 closest distance to " CG  ARG A 269 " =    2.374
peak=   -3.591 closest distance to " CG1 VAL A 250 " =    2.665
peak=   -3.591 closest distance to " O   HOH Z  60 " =    2.527
peak=   -3.587 closest distance to " C   ALA A 158 " =    1.364
peak=   -3.583 closest distance to " CE2 PHE A 218 " =    2.419
peak=   -3.581 closest distance to " ND2 ASN A  45 " =    1.177
peak=   -3.571 closest distance to " CD1 LEU A 101 " =    2.315
peak=   -3.570 closest distance to " CZ  TYR A 169 " =    1.658
peak=   -3.559 closest distance to " O   HOH Z  73 " =    2.143
peak=   -3.559 closest distance to " O   HOH Z 193 " =    1.989
peak=   -3.548 closest distance to " CB  PRO A 163 " =    2.499
peak=   -3.547 closest distance to " CD1 LEU A 228 " =    2.304
peak=   -3.536 closest distance to " O   PRO A 163 " =    2.004
peak=   -3.529 closest distance to " O   HOH Z  38 " =    1.483
peak=   -3.520 closest distance to " CD1 LEU A 297 " =    2.445
peak=   -3.510 closest distance to " O   HOH Z  52 " =    1.278
peak=   -3.508 closest distance to " O   GLY A 211 " =    1.403
peak=   -3.508 closest distance to " CZ BARG A 275 " =    1.818
peak=   -3.508 closest distance to " CA  GLY A 241 " =    3.067
peak=   -3.495 closest distance to " NE2 GLN A 278 " =    1.704
peak=   -3.461 closest distance to " CB  TYR A  15 " =    2.155
peak=   -3.459 closest distance to " OXT GLY A 302 " =    2.868
peak=   -3.448 closest distance to " CD  ARG A 195 " =    5.183
peak=   -3.441 closest distance to " OD1 ASN A 187 " =    1.558
peak=   -3.436 closest distance to " O   ALA A 161 " =    1.692
peak=   -3.433 closest distance to " O   HOH Z 295 " =    1.607
peak=   -3.425 closest distance to " NE2 GLN A 194 " =    1.725
peak=   -3.424 closest distance to " O   HOH Z 359 " =    3.246
peak=   -3.423 closest distance to " O   HOH Z 394 " =    1.401
peak=   -3.407 closest distance to " NH1 ARG A 195 " =    2.565
peak=   -3.407 closest distance to " C   LEU A 143 " =    1.196
peak=   -3.404 closest distance to " N   ALA A 248 " =    1.651
peak=   -3.387 closest distance to " O   HOH Z 243 " =    2.084
peak=   -3.382 closest distance to " O   HOH Z  11 " =    1.740
peak=   -3.378 closest distance to " OD1 ASN A 148 " =    1.538
peak=   -3.375 closest distance to " CA  GLY A 133 " =    2.010
peak=   -3.372 closest distance to " O   ALA A  10 " =    1.641
peak=   -3.371 closest distance to " CB  ALA A 248 " =    2.082
peak=   -3.370 closest distance to " CA  GLY A  98 " =    1.942
peak=   -3.368 closest distance to " NH2 ARG A  79 " =    1.584
peak=   -3.357 closest distance to " SG ACYS A 201 " =    2.009
peak=   -3.348 closest distance to " O   HOH Z 244 " =    2.089
peak=   -3.345 closest distance to " O   HOH Z  51 " =    1.546
peak=   -3.343 closest distance to " O   SER A 135 " =    1.455
peak=   -3.342 closest distance to " CB  ASP A 132 " =    2.273
peak=   -3.341 closest distance to " C   MET A 188 " =    1.346
peak=   -3.339 closest distance to " O   HOH Z 253 " =    3.977
peak=   -3.338 closest distance to " N   SER A 212 " =    1.970
peak=   -3.338 closest distance to " CB  PHE A 208 " =    2.224
peak=   -3.337 closest distance to " O   PHE A 218 " =    1.628
peak=   -3.337 closest distance to " CD2 LEU A 237 " =    2.745
peak=   -3.321 closest distance to " CA  GLY A 241 " =    2.249
peak=   -3.320 closest distance to " O   HOH Z 298 " =    1.270
peak=   -3.319 closest distance to " OD1AASN A 224 " =    1.733
peak=   -3.312 closest distance to " OD2 ASP A 191 " =    1.511
peak=   -3.307 closest distance to " CB  ASP A 286 " =    2.204
peak=   -3.302 closest distance to " OD2 ASP A  50 " =    1.756
peak=   -3.299 closest distance to " O   GLY A  17 " =    1.184
peak=   -3.289 closest distance to " O   HOH Z  44 " =    2.208
peak=   -3.288 closest distance to " O   HOH Z 426 " =    1.583
peak=   -3.287 closest distance to " OE1 GLN A  88 " =    1.157
peak=   -3.286 closest distance to " OD1 ASP A 191 " =    1.574
peak=   -3.285 closest distance to " OD2 ASP A 171 " =    1.824
peak=   -3.280 closest distance to " CG  MET A 105 " =    0.949
peak=   -3.280 closest distance to " N   ASP A 171 " =    2.313
peak=   -3.279 closest distance to " O   HOH Z  93 " =    2.417
peak=   -3.279 closest distance to " O   HOH Z 103 " =    1.906
peak=   -3.275 closest distance to " O   ARG A 145 " =    1.562
peak=   -3.269 closest distance to " CB  LEU A  83 " =    2.423
peak=   -3.267 closest distance to " CD2 TYR A 293 " =    2.008
peak=   -3.266 closest distance to " CB  CYS A 254 " =    2.352
peak=   -3.264 closest distance to " O   HOH Z  13 " =    1.508
peak=   -3.263 closest distance to " O   HOH Z   6 " =    1.457
peak=   -3.262 closest distance to " CD1 ILE A 239 " =    2.395
peak=   -3.259 closest distance to " O   HOH Z 207 " =    2.112
peak=   -3.258 closest distance to " CB  TRP A  85 " =    2.405
peak=   -3.257 closest distance to " O   HOH Z 377 " =    0.871
peak=   -3.256 closest distance to " C   LEU A 222 " =    0.827
peak=   -3.255 closest distance to " O   GLN A 240 " =    2.112
peak=   -3.253 closest distance to " CB  ALA A 248 " =    2.464
peak=   -3.253 closest distance to " CG  TRP A 266 " =    1.865
peak=   -3.251 closest distance to " CA  GLY A 241 " =    2.806
peak=   -3.247 closest distance to " CE3 TRP A 150 " =    2.127
peak=   -3.242 closest distance to " N   THR A 157 " =    1.533
peak=   -3.240 closest distance to " OD1 ASP A 191 " =    1.764
peak=   -3.236 closest distance to " O   VAL A 189 " =    1.566
peak=   -3.231 closest distance to " O   SER A  95 " =    1.519
peak=   -3.228 closest distance to " O   ALA A 180 " =    1.243
peak=   -3.226 closest distance to " CG  GLU A 277 " =    1.190
peak=   -3.226 closest distance to " OG  SER A  62 " =    1.635
peak=   -3.225 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.221 closest distance to " C   PHE A  59 " =    1.383
peak=   -3.221 closest distance to " O   TRP A  70 " =    1.472
peak=   -3.219 closest distance to " CG1 VAL A 197 " =    2.230
peak=   -3.218 closest distance to " O   PRO A 198 " =    1.298
peak=   -3.215 closest distance to " O   HOH Z 114 " =    1.596
peak=   -3.205 closest distance to " NE2 GLN A  88 " =    1.835
peak=   -3.203 closest distance to " CE BMET A  47 " =    1.911
peak=   -3.195 closest distance to " OD2 ASP A 171 " =    2.261
peak=   -3.191 closest distance to " O   HOH Z 166 " =    1.924
peak=   -3.179 closest distance to " OG BSER A 134 " =    1.712
peak=   -3.179 closest distance to " O   HOH Z 322 " =    1.575
peak=   -3.176 closest distance to " O   HOH Z 298 " =    2.501
peak=   -3.174 closest distance to " CG2 VAL A 189 " =    2.025
peak=   -3.172 closest distance to " C   GLN A  58 " =    1.980
peak=   -3.172 closest distance to " O   ALA A 292 " =    2.066
peak=   -3.171 closest distance to " O   HOH Z 310 " =    1.689
peak=   -3.165 closest distance to " O   HOH Z 111 " =    2.023
peak=   -3.163 closest distance to " O   ALA A  51 " =    1.386
peak=   -3.163 closest distance to " CD2 PHE A  61 " =    2.026
peak=   -3.163 closest distance to " N   PHE A  59 " =    2.112
peak=   -3.154 closest distance to " CA  TRP A 274 " =    1.474
peak=   -3.153 closest distance to " CG2 ILE A  20 " =    2.803
peak=   -3.153 closest distance to " OXT GLY A 302 " =    3.346
peak=   -3.152 closest distance to " O   ALA A  34 " =    2.649
peak=   -3.150 closest distance to " CG2 THR A 221 " =    2.259
peak=   -3.148 closest distance to " NH2 ARG A  79 " =    1.991
peak=   -3.146 closest distance to " O   HOH Z 262 " =    2.950
peak=   -3.143 closest distance to " O   HOH Z  88 " =    2.068
peak=   -3.138 closest distance to " CE3 TRP A 274 " =    2.401
peak=   -3.128 closest distance to " OG  SER A 206 " =    1.829
peak=   -3.115 closest distance to " CE  LYS A  76 " =    2.718
peak=   -3.114 closest distance to " O   HOH Z 184 " =    1.796
peak=   -3.098 closest distance to " O   VAL A 174 " =    2.063
peak=   -3.097 closest distance to " O   HOH Z 128 " =    2.567
peak=   -3.088 closest distance to " ND2 ASN A  60 " =    1.419
peak=   -3.084 closest distance to " O   GLN A 240 " =    2.423
peak=   -3.078 closest distance to " O   HOH Z 348 " =    1.833
peak=   -3.071 closest distance to " O   HOH Z  11 " =    2.122
peak=   -3.066 closest distance to " CG  ARG A 269 " =    2.047
peak=   -3.062 closest distance to " CG1 VAL A 125 " =    1.928
peak=   -3.061 closest distance to " CD1 ILE A 199 " =    2.567
peak=   -3.054 closest distance to " C   VAL A 174 " =    1.786
peak=   -3.048 closest distance to " O   HOH Z 281 " =    2.670
peak=   -3.047 closest distance to " CD1 TRP A  70 " =    1.143
peak=   -3.034 closest distance to " O   HOH Z 396 " =    1.721

================= 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    :  0.2454 0.2437   5.794178e+00   5.790410e+00
   1_bss:  0.2290 0.2285   5.760569e+00   5.753379e+00
   1_xyz:  0.1397 0.1584   5.280314e+00   5.394768e+00
   1_adp:  0.1287 0.1610   5.228490e+00   5.413564e+00
   1_occ:  0.1282 0.1609   5.225910e+00   5.412203e+00
   2_bss:  0.1283 0.1600   5.225936e+00   5.410758e+00
   2_xyz:  0.1132 0.1523   5.134385e+00   5.359502e+00
   2_adp:  0.1106 0.1509   5.118082e+00   5.351176e+00
   2_occ:  0.1105 0.1510   5.118203e+00   5.351868e+00
   3_bss:  0.1104 0.1510   5.118036e+00   5.351570e+00
   3_xyz:  0.1118 0.1530   5.131194e+00   5.363928e+00
   3_adp:  0.1104 0.1533   5.127114e+00   5.367415e+00
   3_occ:  0.1103 0.1534   5.127379e+00   5.367970e+00
   4_bss:  0.1103 0.1533   5.127261e+00   5.367809e+00
   4_xyz:  0.1067 0.1536   5.109327e+00   5.365231e+00
   4_adp:  0.1067 0.1532   5.107296e+00   5.362113e+00
   4_occ:  0.1067 0.1533   5.107546e+00   5.362522e+00
   5_bss:  0.1066 0.1534   5.107643e+00   5.362573e+00
   5_xyz:  0.1074 0.1546   5.116451e+00   5.372391e+00
   5_adp:  0.1072 0.1551   5.117344e+00   5.375674e+00
   5_occ:  0.1072 0.1551   5.117517e+00   5.375951e+00
   5_bss:  0.1071 0.1551   5.117606e+00   5.376006e+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:  0.329  54.620  -1.375  -2.177  -1.757  -0.000  -0.000  -0.000
   1_xyz:  0.329  54.620  -1.375  -2.177  -1.757  -0.000  -0.000  -0.000
   1_adp:  0.329  54.620  -1.375  -2.177  -1.757  -0.000  -0.000  -0.000
   1_occ:  0.329  54.620  -1.375  -2.177  -1.757  -0.000  -0.000  -0.000
   2_bss:  0.329  54.620  -2.415  -2.768  -1.773  -0.000  -0.000  -0.000
   2_xyz:  0.329  54.620  -2.415  -2.768  -1.773  -0.000  -0.000  -0.000
   2_adp:  0.329  54.620  -2.415  -2.768  -1.773  -0.000  -0.000  -0.000
   2_occ:  0.329  54.620  -2.415  -2.768  -1.773  -0.000  -0.000  -0.000
   3_bss:  0.330  54.620  -2.459  -2.639  -1.511  -0.000  -0.000  -0.000
   3_xyz:  0.330  54.620  -2.459  -2.639  -1.511  -0.000  -0.000  -0.000
   3_adp:  0.330  54.620  -2.459  -2.639  -1.511  -0.000  -0.000  -0.000
   3_occ:  0.330  54.620  -2.459  -2.639  -1.511  -0.000  -0.000  -0.000
   4_bss:  0.325  54.620  -2.374  -2.505  -1.328  -0.000  -0.000  -0.000
   4_xyz:  0.325  54.620  -2.374  -2.505  -1.328  -0.000  -0.000  -0.000
   4_adp:  0.325  54.620  -2.374  -2.505  -1.328  -0.000  -0.000  -0.000
   4_occ:  0.325  54.620  -2.374  -2.505  -1.328  -0.000  -0.000  -0.000
   5_bss:  0.325  54.620  -2.182  -2.304  -1.105  -0.000  -0.000  -0.000
   5_xyz:  0.325  54.620  -2.182  -2.304  -1.105  -0.000  -0.000  -0.000
   5_adp:  0.325  54.620  -2.182  -2.304  -1.105  -0.000  -0.000  -0.000
   5_occ:  0.325  54.620  -2.182  -2.304  -1.105  -0.000  -0.000  -0.000
   5_bss:  0.325  54.593  -1.980  -2.102  -0.897  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  23.065 0.8358  0.9925    16457.264
   1_bss:  21.830 0.8466  0.9459    13806.506
   1_xyz:  14.017 0.9154  0.9898     6526.530
   1_adp:  14.461 0.9115  0.9888     6720.269
   1_occ:  14.429 0.9117  0.9887     6677.155
   2_bss:  14.386 0.9120  0.9695     6651.702
   2_xyz:  13.326 0.9204  0.9740     6019.826
   2_adp:  13.151 0.9218  0.9723     5884.539
   2_occ:  13.166 0.9217  0.9721     5891.066
   3_bss:  13.162 0.9217  0.9762     5886.961
   3_xyz:  13.342 0.9206  0.9744     6054.826
   3_adp:  13.418 0.9200  0.9689     6070.308
   3_occ:  13.433 0.9199  0.9687     6077.710
   4_bss:  13.431 0.9199  0.9734     6073.278
   4_xyz:  13.393 0.9201  0.9738     6056.861
   4_adp:  13.333 0.9205  0.9684     6022.565
   4_occ:  13.343 0.9204  0.9683     6026.595
   5_bss:  13.346 0.9204  0.9755     6027.636
   5_xyz:  13.500 0.9194  0.9746     6158.130
   5_adp:  13.565 0.9189  0.9676     6186.620
   5_occ:  13.571 0.9188  0.9675     6189.398
   5_bss:  13.573 0.9188  0.9737     6190.571
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6010e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6010e-01
   1_xyz:   0.979  0.007  0.072 15.243  0.004  4.115   5.8577e-02
   1_adp:   0.979  0.007  0.072 15.243  0.004  4.115   5.8577e-02
   1_occ:   0.979  0.007  0.072 15.243  0.004  4.115   5.8577e-02
   2_bss:   0.979  0.007  0.072 15.243  0.004  4.115   5.8577e-02
   2_xyz:   1.029  0.009  0.080 15.242  0.004  4.118   6.6875e-02
   2_adp:   1.029  0.009  0.080 15.242  0.004  4.118   6.6875e-02
   2_occ:   1.029  0.009  0.080 15.242  0.004  4.118   6.6875e-02
   3_bss:   1.029  0.009  0.080 15.242  0.004  4.118   6.6875e-02
   3_xyz:   0.921  0.007  0.072 15.033  0.003  4.119   5.4815e-02
   3_adp:   0.921  0.007  0.072 15.033  0.003  4.119   5.4815e-02
   3_occ:   0.921  0.007  0.072 15.033  0.003  4.119   5.4815e-02
   4_bss:   0.921  0.007  0.072 15.033  0.003  4.119   5.4815e-02
   4_xyz:   1.046  0.009  0.081 15.236  0.004  4.120   6.8580e-02
   4_adp:   1.046  0.009  0.081 15.236  0.004  4.120   6.8580e-02
   4_occ:   1.046  0.009  0.081 15.236  0.004  4.120   6.8580e-02
   5_bss:   1.046  0.009  0.081 15.236  0.004  4.120   6.8580e-02
   5_xyz:   0.992  0.008  0.077 15.106  0.004  4.120   6.2497e-02
   5_adp:   0.992  0.008  0.077 15.106  0.004  4.120   6.2497e-02
   5_occ:   0.992  0.008  0.077 15.106  0.004  4.120   6.2497e-02
   5_bss:   0.992  0.008  0.077 15.106  0.004  4.120   6.2497e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4160e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4160e-01
   1_xyz:   8.049  0.036  0.244 84.448  0.037  2.372   4.4401e-02
   1_adp:   8.049  0.036  0.244 84.448  0.037  2.372   4.4401e-02
   1_occ:   8.049  0.036  0.244 84.448  0.037  2.372   4.4401e-02
   2_bss:   8.049  0.036  0.244 84.448  0.037  2.372   4.4401e-02
   2_xyz:   7.228  0.044  0.261 84.364  0.035  2.270   5.7578e-02
   2_adp:   7.228  0.044  0.261 84.364  0.035  2.270   5.7578e-02
   2_occ:   7.228  0.044  0.261 84.364  0.035  2.270   5.7578e-02
   3_bss:   7.228  0.044  0.261 84.364  0.035  2.270   5.7578e-02
   3_xyz:   7.269  0.040  0.222 84.206  0.034  2.384   3.9802e-02
   3_adp:   7.269  0.040  0.222 84.206  0.034  2.384   3.9802e-02
   3_occ:   7.269  0.040  0.222 84.206  0.034  2.384   3.9802e-02
   4_bss:   7.269  0.040  0.222 84.206  0.034  2.384   3.9802e-02
   4_xyz:   6.998  0.045  0.262 84.120  0.037  2.288   5.1564e-02
   4_adp:   6.998  0.045  0.262 84.120  0.037  2.288   5.1564e-02
   4_occ:   6.998  0.045  0.262 84.120  0.037  2.288   5.1564e-02
   5_bss:   6.998  0.045  0.262 84.120  0.037  2.288   5.1564e-02
   5_xyz:   7.093  0.045  0.246 83.852  0.037  2.333   4.5677e-02
   5_adp:   7.093  0.045  0.246 83.852  0.037  2.333   4.5677e-02
   5_occ:   7.093  0.045  0.246 83.852  0.037  2.333   4.5677e-02
   5_bss:   7.093  0.045  0.246 83.852  0.037  2.333   4.5677e-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:  62.93   0.00  16.47  52.44   0.00  12.67  62.93   6.85  37.13
   1_occ:  62.93   0.00  16.47  52.44   0.00  12.67  62.93   6.85  37.13
   2_bss:  62.93   0.00  16.47  52.44   0.00  12.67  62.93   6.85  37.13
   2_xyz:  62.93   0.00  16.47  52.44   0.00  12.67  62.93   6.85  37.13
   2_adp:  65.73   2.13  16.57  65.34   2.13  12.84  65.73   5.79  36.86
   2_occ:  65.73   2.13  16.57  65.34   2.13  12.84  65.73   5.79  36.86
   3_bss:  65.73   2.13  16.57  65.34   2.13  12.84  65.73   5.79  36.86
   3_xyz:  65.73   2.13  16.57  65.34   2.13  12.84  65.73   5.79  36.86
   3_adp:  73.73   1.26  16.81  73.73   1.26  12.86  69.29   6.44  38.31
   3_occ:  73.73   1.26  16.81  73.73   1.26  12.86  69.29   6.44  38.31
   4_bss:  73.73   1.26  16.81  73.73   1.26  12.86  69.29   6.44  38.31
   4_xyz:  73.73   1.26  16.81  73.73   1.26  12.86  69.29   6.44  38.31
   4_adp:  75.19   1.27  16.62  75.19   1.27  12.70  70.44   6.49  37.99
   4_occ:  75.19   1.27  16.62  75.19   1.27  12.70  70.44   6.49  37.99
   5_bss:  75.19   1.27  16.62  75.19   1.27  12.70  70.44   6.49  37.99
   5_xyz:  75.19   1.27  16.62  75.19   1.27  12.70  70.44   6.49  37.99
   5_adp:  76.06   0.81  16.50  76.06   0.81  12.54  70.81   6.10  38.07
   5_occ:  76.06   0.81  16.50  76.06   0.81  12.54  70.81   6.10  38.07
   5_bss:  76.03   0.79  16.47  76.03   0.79  12.51  70.78   6.08  38.05
------------------------------------------------------------------------
 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:    0.553    0.011    0.211
   1_adp:    0.553    0.011    0.211
   1_occ:    0.553    0.011    0.211
   2_bss:    0.553    0.011    0.211
   2_xyz:    0.616    0.014    0.243
   2_adp:    0.616    0.014    0.243
   2_occ:    0.616    0.014    0.243
   3_bss:    0.616    0.014    0.243
   3_xyz:    0.804    0.027    0.249
   3_adp:    0.804    0.027    0.249
   3_occ:    0.804    0.027    0.249
   4_bss:    0.804    0.027    0.249
   4_xyz:    0.867    0.030    0.256
   4_adp:    0.867    0.030    0.256
   4_occ:    0.867    0.030    0.256
   5_bss:    0.867    0.030    0.256
   5_xyz:    1.017    0.035    0.260
   5_adp:    1.017    0.035    0.260
   5_occ:    1.017    0.035    0.260
   5_bss:    1.017    0.035    0.260
------------------------------------------------------------------------

CPU time actual refinement: 322.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_896/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_896/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_896/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_896/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_896/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.75 
  Macro-tasks:
    bulk solvent and scale       = 36.16  
    individual site refinement   = 139.35 
    weights calculation          = 28.73  
    collect and process          = 6.46   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.82 
  Micro-tasks:
    mask                            = 0.62   
    f_calc                          = 102.83 
    alpha_beta                      = 8.35   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 113.94 
    fmodel                         = 6.58   
    r_factors                      = 0.18   
    phase_errors                   = 10.99  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 244.96 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.490 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    660 calls, 102.46 s
gradients_fft:          605 calls,  99.36 s

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

# Date 2008-01-16 Time 05:55:02 PST -0800 (1200491702.11 s)
Start R-work = 0.2454, R-free = 0.2437 (no bulk solvent and anisotropic scale)
Final R-work = 0.1307, R-free = 0.1738 (no bulk solvent and anisotropic scale)

Start R-work = 0.2290, R-free = 0.2285
Final R-work = 0.1071, R-free = 0.1551